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Copies of the agreement, released late Sunday, outline the powers that will be reserved by the national government, those that will held by the government of the autonomous area and those that will be shared by both.
The accord also sets the parameters of the "Bangsamoro assembly" that will govern the autonomous area while ensuring that tribal groups, Christian settlers and women are represented.
While foreign policy, defence, monetary policy, immigration and global trade will remain under the control of national government, the Bangsamoro government will have powers over agriculture, employment, urban development, public works and environmental protection, the agreement said.
In an interview with ABS-CBN television, Deles described the move to power-sharing as "the heart of the entire peace accord."
The two sides in October last year had signed an initial pact on ending the conflict that has claimed an estimated 150,000 lives, in preparation for a final agreement.
Under the plan, the 12,000-strong MILF would give up its quest for an independent homeland in the southern island of Mindanao in return for significant power and wealth-sharing in a new autonomous region there.
Lingering obstacles
The newly-signed power sharing annex had been one of four preliminary accords that had to be completed before a final peace deal could be signed.
Two other annexes on transitional arrangements and sharing of revenues had already been signed earlier this year while a fourth annex, on normalisation, including the possible disarming of MILF guerrillas, is still being discussed.
The normalisation annex may also prove difficult as the rebels will likely be reluctant to lay down their arms.
MILF negotiator Mohagher Iqbal was quoted by ABS-CBN as saying that the next round of talks would also be difficult and that both sides should not be complacent.
Even after the treaty is signed, the Philippine parliament would still need to pass a "basic law" for the Muslim self-rule area, and people in the planned autonomous region would need to ratify it via a regional plebiscite.
However President Aquino in October had expressed confidence that the insurgency could be settled before he steps down in 2016.
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