Israel has reacted angrily to Austria's decision to withdraw its peacekeeping forces from the Golan Heights, saying the move has undermined the authority of the United Nations as the Syrian civil war threatens to spill over the border into Israel.

Israeli officials say the withdrawal of Austrian troops from the peacekeeping force monitoring the demilitarised border area following the injury of a Filipino soldier during clashes on Thursday threatened the role of the UN Security Council in any future negotiations between Israel and the Palestinians.

In a statement issued late on Thursday afternoon, Austria announced its decision to remove all 380 of its troops from the 1,000-strong force on the Israel-Syrian border due to the "continuing deterioration of the situation in the area".

"Austrian soldiers face an uncontrollable and direct threat, which has increased to an unacceptable level. The development in the early morning hours of today has shown that it is no longer justifiable to watch and wait," said the statement issued by Werner Faymann, Austria's federal chancellor, and Michael Spindelegger, vice-chancellor, of its mission in the Golan.

Syrian rebels groups briefly seized control of the Quneitra border crossing after hours of sustained and intense fighting with tanks and artillery, during which several shells exploded inside Camp Ziouni, a UN compound inside the demilitarised zone, and three mortars reportedly exploded inside Israeli-occupied territory.

During this time, the likelihood of Israeli forces entering Syrian territory to secure their border was higher than at any point since 1974. Israeli military action was averted, officials said, because the Syrian president, Bashar Assad, won and took back control of the crossing.

In Israel, the troop withdrawal was read as a betrayal of the United Nation's commitment to regional security, pledged during Israeli disengagement from Syria in 1974. Austria, along with troops from India and the Philippines, has provided a critical portion of the United Nations Disengagement Observer Force (Undof) charged with ensuring quiet on this sensitive border for the past 40 years.

"The only reason you want anyone there in the first place is in time of trouble," one senior Israeli official told the Guardian. "For the first time in 40 years, it's not easy so the presence ends? That sends a very problematic message to the Israeli public.

"This means that in any future deal with the Palestinians, we won't accept any disengagement forces from the United Nations because at the first sign of trouble, they'll disappear."

A more reserved statement issued by Israel's foreign ministry expressed its regret at Austria's decision and hoped that "it will not be conducive to further escalation in the region".

"Israel expects the United Nations to uphold its commitment under Security Council Resolution 350 (1974), in virtue of which Undof has been established," it concluded. Israeli officials made it clear they expected the Security Council to fill the gap left by the Austrian troops swiftly.

Thursday's battle marked a crescendo in the clashes between two Syrian regime brigades and a collection of Jihadist and rebel groups wrestling for control of the northern Golan. Fighting alongside the al-Qaeda allied al-Nusra front is a group of Iraqi jihadists calling itself the Quneitra Liberation Front, which claimed responsibility for a string of car bomb attacks on regime intelligence posts. The Yarmouk Martyrs Brigade, responsible for the recent kidnapping of Filipino peacekeepers, is also established in the area.

As the only crossing point between Syria and Israeli-occupied Golan, Quneitra not only holds substantial symbolic importance but is of strategic importance to both sides. It is the only city on the Israeli Syrian border, marking a critical point on the arms supply route between Lebanon rebel groups, and an important gateway to the Alawite communities in the south for Damascus.

As regime forces battled for Quneitra, sporadic fighting between Hezbollah and rebel groups continued in villages north of Qusair on Thursday. Qusair fell to Hezbollah on Wednesday in a significant victory for the government over the rebels. The Syrian army also shelled several villages in which rebels had sought refuge south of the country's third city, Homs. A rebel spokesman, Abu Imad, said the fleeing fighters had 200 wounded with them and that they feared being trapped and killed.

"We are in the north side of Qusair," he said. "And fighting hasn't stopped. They are still chasing us and firing artillery. We are having a major problem evacuating the wounded people."

Hezbollah's lead role in the battle for Qusair is widely seen as a harbinger of a broader role for the Lebanese Shia militia in Syria, having instilled momentum into a regime military that had struggled to gain ground in many parts of the country since last summer.

Rebel leaders in Aleppo said they had concrete intelligence that small numbers of Hezbollah forces were already deployed in Shia villages to the north of the city – Syria's largest – which has been split more or less down the middle since a rebel incursion last July.

"They are coming for Aleppo soon, we know that for sure," the rebel leader, a commander of Aleppo's largest militia, Liwa al-Tawheed, said. "They will need to bypass Homs and Hama to get here and they can only take the highway, so we will know when they start to move. We are expecting a battle before Ramadan." The Muslim holy month is due to start sometime around mid-July.

Hezbollah specialises in urban warfare, a form of combat in which the Syrian Army receives little training. "They do not do fire and manoeuvre well, the Syrians," said a Lebanese general who did not want to be named said. "They follow the Soviet doctrine of standing off and pummelling a battlefield and then eventually going in, but only if they have to.

"Hezbollah train heavily for battles in urban environments under artillery cover. They could shift the balance in Aleppo, where the regime has failed to do so."

While Qusair was hailed as a strategic crossroads for both sides, a fight for Aleppo would prove far more instructive in the eventual outcome of the civil war, which is now four months into its third year.

Arab states, especially Saudi Arabia and Qatar have reacted furiously to Hezbollah's large and public role in Qusair and have vowed to provide rebel groups with weapons they need to hold the parts of the country they have seized. The main opposition supply lines run through southern Turkey, which is close to Aleppo and within easy reach for the myriad rebel groups who would lead the defence of the city.

The initial success of rebel forces at Quneitra, who not only seized the Syrian section of the border crossing point but destroyed four Syrian army tanks in the process, sent shockwaves through the Israeli security establishment. The IDF declared the border area a military zone. Road 98, an arterial highway running along the armistice line, was closed. Farmers were forbidden from tending their fruit orchards. Kibbutz residents were ordered to stay inside their homes.

The removal of the Austrian troops has undoubtedly shaken Israeli confidence. In their absence, if the Israeli Air Force should launch another strike on a Syrian regime arms convoy bound for Lebanon and the Assad regime feels obliged to enact its promise to retaliate, the Golan Heights, as a pan-Arabic cause mentioned several times by the Hezbollah leader, Nasrallah, in his most recent speech, would be an obvious spot to attack. Israeli intelligence reports that Iranian and Hezbollah reinforcements are already supporting the regime in the Golan.

But while Assad may be winning the battle for Syria on the ground, Israel's analysis remains that he cannot spare the military energy to open a new front with Israel.

"The regime has assured us of quiet on the Golan border for 40 years. Now it seems we have someone in control of that border who has their back to us now but may turn around and face us at any point," a senior Israeli official said, speaking on condition of anonymity.

"The message [the Austrian withdrawal] has sent to Israelis is that at the end of the day, we can only rely on ourselves. The IDF is big, strong, ugly and it is reliable. It is us and our kids."