The power sharing annex had been considered as one of the most contentious with Moro Islamic Liberation Front (MILF) rebels seeking greater authority over a proposed autonomous region in the south which will cover Muslim-dominated regions of this mainly-Catholic archipelago of 100 million.
A joint statement said negotiators from the government and MILF had signed "the agreement on the delineation and sharing of power between the central government and the Bangsamoro (Filipino Muslim) government" in Kuala Lumpur on Sunday.
The terms of the completed power sharing agreement were not immediately known. The statement added that both parties were now "confident" that they could soon sign the last remaining annex on normalisation and complete the "comprehensive peace agreement" by January 2014.
"The signing of the Annex on Power Sharing ensures the achievement of a genuine and viable autonomy for the Bangsamoro," Teresita Deles, the head of the government peace panel, said.
"It has been a very difficult round but we were able to overcome a lot of obstacles."
President Benigno Aquino congratulated both parties on the annex, his spokesman Herminio Coloma said.
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.
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.
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.
Completing the agreement during Aquino's term is considered vital as he is limited to only one term and there is no guarantee his successor would have the political strength or enthusiasm to push ahead with the peace process.
Muslim rebels have been fighting since the 1970s for an autonomous or independent homeland in the southern Philippines in a conflict that has left the resource-rich region mired in poverty and instability.