The Philippine government and the country's largest Muslim rebel group signed a historic peace agreement Thursday following 17 years of negotiations and decades of fighting that killed at least 120,000 in the southern island of Mindanao.

The deal between the government of President Benigno Aquino III and the Moro Islamic Liberation Front (MILF) was signed at the presidential palace in the capital, Manila, and will grant largely Muslim areas of the Mindanao region greater political autonomy in exchange for an end to armed rebellion and dropping its claims for a separate state.

An existing five-province Muslim autonomous region will be replaced by a more powerful, better-funded and potentially larger region, to be called Bangsamoro.

The new Bangsamoro government will receive 75 percent of taxes collected in the region, as well as 75 percent of revenues from metallic minerals and some control of fishing territories.

"Let us cast aside past prejudices and contribute to the atmosphere of optimism that has for the first time in a long while become prevalent in Muslim Mindanao," Aquino said before the signing.

Previous presidents have tried and failed to resolve the conflict, which has stunted growth in the region and helped foster Islamic extremism in the country and elsewhere in Southeast Asia.

Malaysian Prime Minister Najib Razak, whose country brokered the peace talks, attended the ceremony.

"In signing this agreement, the two sides have looked not to the problems of the past, but to the promise of the future," Najib said. "After so many years of conflict and so many lives lost, it is a momentous act of courage."

As part of the deal, the MILF promised to turn in the weapons of the 10,000 to 15,000 rebel fighters, considered the biggest armed group in Southeast Asia.

The original rebel group Moro National Liberation Front, which signed a separate agreement in 1996, and the Bangsamoro Islamic Freedom Fighters, who are fighting for an independent state, are excluded from the deal.

The agreement will not end all violence in a part of the country long plagued by lawlessness, poverty and Islamist insurgency.

Other insurgent groups have vowed to keep fighting for full independence. The region is also home to the Abu Sayyaf, a Muslim extremist network with international links that the Philippine army is battling with American support.

The peace accord concludes formal negotiations that began in 2001. A cease-fire agreement had been in place since 1997 and has been largely observed by both sides.

Separatist violence has raged since the 1970s in Mindanao, the main southern Philippine island. It is home to most of the country's 5 million Muslims, but Christians remain the overall majority.

Much work remains to ensure that the terms of the deal and the political framework it envisages are implemented fully during the remainder of Aquino's term, which ends in 2016.

Al Jazeera's Ted Regencia contributed to this report, with wire services.