The central government will oversee defence, security, and foreign and monetary policy, and soon appoint a transition authority nominated by the Moro Islamic Liberation Front (MILF).
Vice President Leni Robredo said it was vital the central government helps Bangsamoro to build “a progressive economy and responsible local government”.
“Let us guard and support the progress of this process because this is not yet the end of the fight for peace,” Mrs Robredo said.
The vote came at a critical time for the Philippines, which saw disillusioned MILF factions break away and follow other armed groups in pledging allegiance to Islamic State of Iraq and the Levant (ISIL).
That has stoked fears that fighters fleeing Iraq and Syria would join radicals from Malaysia and Indonesia in gravitating to Mindanao to capitalise on porous borders, jungles and mountains, and an abundance of arms.
Martial law has been in place in Mindanao since an extremist alliance overran Marawi City in 2017 and occupied it for five months, in what was the Philippines’ fiercest and longest conflict since World War Two.
The army said three remnants of that alliance were killed on Thursday when troops discovered a makeshift jungle camp. It released images of trenches and what it said was ISIL paraphernalia.