Exactly five years ago, President Obama first called for Syrian President Bashar Assad to step down, a demand that has proved uniquely futile in a brutal civil war that this week expanded to include Russian warplanes using a base in Iran to launch bombing runs in support of Mr. Assad’s regime.

It was on Aug. 18, 2011, that Mr. Obama first declared publicly that it was “time for the Syrian people to determine their own destiny, and we will continue to stand firmly on their side.” Administration officials argued there could be no lasting peace so long as Mr. Assad, with so much blood on his hands, remained in power.

Rather than relinquish power, however, Mr. Assad dug in. While the U.S. has mostly sat on the sidelines militarily since then, more than 450,000 Syrians have died in the civil war, and Mr. Assad increasingly has relied on Russia to help him in the fight.

On Wednesday, in a move that could have aftershocks felt across the Middle East, Iran confirmed that Russia is using its territory to launch airstrikes in Syria even as a second wave of Moscow’s bombers flew out of the Islamic republic to hit targets in the war-ravaged country.

Moscow’s action deepened its involvement in the civil war and angered the U.S., which said the move might violate a U.N. Security Council Resolution prohibiting the supply or transfer of military aircraft to Tehran.

Russian Foreign Minister Sergei Lavrov said on Wednesday that any U.S. dismay over Moscow’s military cooperation with Iran should not distract from efforts to reach the U.S.-Russia deal on coordinating action in Syria and securing a cease-fire.

The Kremlin, showing little regard for U.S. concerns, argued there were no grounds to suggest Russia’s actions had violated the U.N. resolution, saying Moscow was not supplying Iran with military aircraft for its own internal use, something the document prohibits.

“It’s against our rules to provide advice to the leadership of the U.S. State Department,” Maj. Gen. Igor Konashenkov, spokesman for Russia’s Defense Ministry, said in a statement Wednesday, “but it’s hard to resist a recommendation for some State Department representatives to check their logic and knowledge of fundamental documents of international law.

“Moreover, we again advise the State Department representatives to take a pencil to the map and discover for themselves that Syria is an independent sovereign state,” the general added.

Russia first announced the strikes on Tuesday from near the Iranian city of Hamedan, 175 miles southwest of Tehran. On Wednesday, Russia’s Defense Ministry said another wave of bombers had departed from Iran, striking targets in eastern Syria.

Alaeddin Boroujerdi, the head of the Iranian parliament’s national security and foreign policy committee, said the Russians were using Iran’s Shahid Nojeh air base some 30 miles north of Hamedan, a secluded base where Russian warplanes were detected landing late last year.

Mr. Boroujerdi said the Russian Tu-22M3 fighter jets landed inside Iran only to refuel under the permission of the country’s Supreme National Security Council, a move that allowed them to carry a larger bomb load of more than 20 metric tons. While Moscow and Tehran have combined to be the two biggest backers of the embattled Mr. Assad, there were no plans for a permanent base, the Iranian lawmaker said.

“There is no stationing of Russian forces in the territory of the Islamic Republic of Iran,” he added.

Russia’s use of the Iranian air base comes amid intense fighting for the Syrian city of Aleppo, where rebels are battling Syrian government forces backed by the Russian military, and as Moscow and Washington are working toward a deal on Syria that could see them cooperate more closely.

Dashed expectations

Mr. Obama’s public shaming of Mr. Assad five years ago, and his declaration in 2012 of a “red line” against the use of chemical weapons in Syria, raised expectations that the U.S. would take strong actions to topple the Syrian regime, said Jim Phillips, a specialist on the Middle East at the conservative Heritage Foundation. Instead, the administration limited its response to humanitarian aid and sanctions, and didn’t attack the regime when Mr. Assad’s forces used chemical weapons against pro-Western rebel forces.

“Raising expectations without taking any effective action to meet those expectations had a demoralizing effect on the Syrian opposition, which increasingly looked to Sunni Islamist extremist groups for protection against the brutal Assad regime,” Mr. Phillips said. “The president’s failure to back his call with effective action also undoubtedly undermined his own credibility and encouraged the Assad regime to violate his August 2012 ‘red line’ against the use of chemical weapons.”

The White House didn’t respond to a request for comment on the impact of Mr. Obama’s calls for Mr. Assad to step down. The president has acknowledged he’s not satisfied with the situation in Syria, but has defended his decision not to get involved in another ground war in the Middle East and to delay arming opposition groups until they could be vetted. He has also predicted Russian President Vladimir Putin would regret his decision to intervene in the Syrian conflict.

After pulling back from a contemplated missile attack against Mr. Assad in 2012, Mr. Obama accepted the help of Russia to negotiate the removal of Mr. Assad’s chemical weapons stockpile. However, other attacks involving chemical weapons have been alleged, one as recently as June.

The situation around Aleppo has grown so dire that a group of the city’s doctors wrote a letter to Mr. Obama last week begging for shipments of medical supplies.

“We do not need tears or sympathy or even prayers,” they wrote. “We need action. We have seen no effort on behalf of the United States to lift the siege or even use its influence to push the parties to protect civilians.”

The administration has spent nearly $5.6 billion on humanitarian aid for Syrians since the civil war began. Mr. Obama also signed legislation in 2014 for the Pentagon to train and equip moderate Syrian rebels, an effort that failed to produce more than a handful of fighters.

The U.S. also has airlifted tons of weaponry to opposition groups in northern Syria. And Mr. Obama has deployed small numbers of U.S. special forces to Syria to fight the Islamic State, in addition to the thousands of airstrikes that the U.S.-led coalition has launched against the extremist group operating in Syria and Iraq.

Mr. Phillips said the actions taken against Mr. Assad have proved to be “too little, too late.”

“Now the administration is exploring the possibility of coordinating air campaigns with Russia, despite the fact that the Russians target moderate Syrian rebel groups, some of them supported by the U.S., more than they target the Islamic State or al Qaeda in Syria,” he said. “This will further tarnish U.S. credibility with Syrian rebel groups and U.S. allies in the Middle East.”

Russia’s use of an Iranian base heralds even more intense Russian bombardment inside Syria, where Moscow has already been accused of indiscriminate attacks that have killed many civilians.

On Wednesday, presumed Russian or Syrian government airstrikes on the rebel-held city of Idlib in the northwest killed 17 people and wounded at least 30 others, the Civil Defense branch for the province reported. A video posted on the group’s website showed rescue workers pulling bodies from wreckage along a heavily damaged street. The Syrian Observatory for Human Rights also reported the strikes, saying dozens of civilians were killed and wounded.

For Iran, allowing Russia to launch strikes from inside the country is likely to prove unpopular. Many still remember how Russia, alongside Britain, invaded and occupied Iran during World War II to secure oil fields and Allied supply lines.

• This article is based in part on wire-service reports.

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