In return, the bloc will lift trade and economic sanctions and grant amnesty to the ruling junta, mediators said.
The move came after Tuareg rebels in the north declared independence of territory they call Azawad.
The rebels seized the area after a coup two weeks ago plunged the West African nation into political crisis.
Under the terms of transition plan, military rulers will cede power to the parliamentary speaker, Diouncounda Traore, who as interim president will oversee a timetable for elections.
Once sworn in, Mr Traore would have 40 days to organise elections, the five-page agreement says.
After four days of total embargo, the announcement will certainly comes as a relief for the Malian population.
However, it doesn't specify when Captain Amadou Sanogo would effectively hand over power to the head of the national assembly.
The sooner the better. The northern crisis will probably not be addressed before a legitimate government is in place in Bamako but the situation is now critical.
Tuareg-led rebels have declared independent a vast land of lawlessness and confusion from which at least half the population, already impoverished, fled either south or across borders into neighbouring countries.