The deal would establish a regional government that would have greater autonomy over taxes, the use of natural resources and, in exchange, the Moro Islamic Liberation Front, or MILF, would begin disarming its force of 11,000 rebels.
Negotiations will be held in Malaysia next month to finalize the details of the agreement.
The government said the proposed region, to be known as Bangsamoro, would have more autonomy but would not become independent from the predominantly Catholic nation.
While the peace deal may be viewed as an accomplishment for the administration of Benigno Aquino, other Muslim rebel groups remain in the region and may encourage members of MILF to abandon the group and join their forces.
However, at least one prominent foreign dignitary hailed the agreements.
Speaking at the signing ceremony as part of his first official visit to the Philippines, the Prime Minister of Malaysia Najib Razak (who is Muslim) said the framework agreement ushers in a new era of peace where “people of different faiths live together, united by common values, under a common constitution.”
He added: “In confronting their differences and finding common ground, both sides have given something. But the people of the Southern Philippines have gained everything. In choosing peace over conflict, and stability over chaos, both sides have stated their belief not just in universal principles of democracy, justice, and tolerance, but in their application in the service of a greater good.
“In years to come, I believe all those involved will look back and see that their hands laid the foundations for an enduring peace. That their willingness to give, and to forgive, made possible a better future for all.”