The resignation was given to West African mediators in the capital city of Bamako, said a spokesman for Dioncounda Traore, the speaker of the parliament.
After spending more than two weeks in neighboring Burkina Faso, Traore returned to Bamako on Saturday. He is expected to lead a transitional government, though it was not immediately clear when he will take office.
He called for unity in remarks made on state television Friday.
In a significant sign of success of international pressure, West African nations have lifted sanctions imposed on Mali after an agreement on restoring constitutional order.
A statement distributed Sunday from the Economic Community of West African States (ECOWAS) said it "has decided to lift all the sanctions imposed on Mali with immediate effect."
The statement was signed by Ivorian President Alassane Ouattara, who chairs the group.
Junta leader Capt. Amadou Sanogo reached a deal with ECOWAS that mandated a handover of power to the civilian government in exchange for the end of trade and diplomatic sanctions.
The deal was announced late Friday on Mali state television.
The March 22 coup staged by renegade soldiers sparked a crisis in Mali, a west African nation that had been a cornerstone of stability.
The international community -- including West African states, the African Union and the United States -- called for the immediate restoration of constitutional rule.
Adding to the chaos are separatist Tuareg rebels who capitalized on the post-coup disorder and captured large areas of Mali's vast Sahara region in the north. They declared independence for a region they recognize as Azawad, the cradle of their nomadic civilization.
The rebels have effectively split the West African nation in two, and northern areas remain volatile and tense, preventing aid agencies from accessing displaced people, the United Nations refugee agency said.
The African Union and ECOWAS had slapped the military junta in Bamako with travel and economic restrictions, and froze its assets.
Under the sanctions, five neighboring nations were to close their borders to landlocked Mali except for humanitarian purposes and deny the nation access to their ports, freeze its accounts in regional banks and suspend its participation in cultural and sporting events.
Friday's agreement and the end of the ECOWAS sanctions brought fresh hope this weekend that Mali would return to democratic governance.
Once a constitutional government is restored, France -- the former colonial power in Mali -- will resume military and civil cooperation with Mali, according to the French foreign ministry.
France will help the future government find a political solution to the problems in Tuareg-controlled areas in the north, the ministry said. France also urged the rebel leaders to seek a political resolution.
