The submission to Congress is seen as significant as it means Aquino and the Moro Islamic Liberation Front (MILF) have agreed, after months of tense talks, on the entire legal underpinning for Muslim self-governance in the southern region of Mindanao.
"We have taken yet another step towards a more peaceful and more progressive Mindanao," Aquino said after turning over the bill to congressional leaders.
He called for the passage "in the soonest possible time" of the proposed law that would have MILF leaders governing a region comprising about 10 percent of the Philippines' land area.
Under the timetable of a peace pact, the law is meant to be passed before the end of this year, giving Aquino time to put in place a regional government before his six-year term ends in mid-2016.
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Once the law is passed, its residents would have to endorse it in a plebiscite scheduled for 2015.
The agreement separately calls on the MILF to disarm under supervision by international monitors.
Both Senate President Franklin Drilon and opposition Senator Ferdinand Marcos Jnr. Said the bill has broad support, though they warned there may not be enough time for it to pass this year.
The rebellion began more than 40 years ago when Marcos's late father Ferdinand Marcos Snr. Was president, and has since claimed tens of thousands of lives.
The 10,000-strong MILF is worried over delays in drafting the bill, but trusts it will be passed within the agreed timetable, its chief negotiator Mohagher Iqbal said.
The United Nations office in Manila congratulated the two sides and said it stood ready to support the implementation of the law.