President Amadou Toumani Toure of Mali has formally resigned as part of a deal with coup leaders to end the crisis gripping the West African state.
International mediator Djibril Bassole, Burkina Faso's foreign minister, confirmed a letter of resignation had been submitted.
The resignation paves the way for the coup leaders to step aside and the parliamentary speaker to take over.
Mali has been grappling with a separatist uprising in the north.
It intensified after the coup by army officers on 22 March.
Mr Bassole, who represents the West African regional bloc Ecowas, met Mr Toure in the Malian capital, Bamako.
"We have just received the formal letter of resignation from President Amadou Toumani Toure," he told reporters.
"We will now contact the competent authorities so that the vacancy of the presidency would be established and so that they take the appropriate measures."
Under the agreement, the Malian parliamentary speaker, Dioncounda Traore, will take over as interim president and govern with a transitional administration until elections are held.
Once he has been sworn in, Mr Traore has 40 days to organise this poll, the deal stipulates.
Mr Traore, who has been in Burkina Faso since the coup was launched, said as he left for Bamako: "I am leaving for Mali with my heart full of hope.
"My country has known enormous difficulties, but I am leaving with the hope the people of Mali will come together to face this adversity head-on."
Ecowas has lifted sanctions it imposed after the coup and an amnesty has been agreed for the coup leaders.
The coup, led by Capt Amadou Sanogo, took place amid accusations from the army that the government had not done enough to supress the insurrection in the north.
Since the coup, key towns in northern Mali have fallen to Tuareg separatist rebels and their Islamist allies.
The Tuaregs have called for their newly-named territory of Azawad to be recognised as independent, although this has been rejected by the international community.
There are two main groups behind the rebellion: the secular National Movement for the Liberation of Azawad (MNLA) and Ansar Dine, an Islamist group.
The MNLA is made up partly of Tuaregs who had fought in Libya on the side of Col Muammar Gaddafi and returned to Mali after he was killed.
The latter has started to impose Sharia law in some towns.
Among the towns to have fallen to the Tuaregs is Timbuktu, the 1,000-year-old desert city which is now a Unesco World Heritage site.
Unesco warned that the fighting could damage Timbuktu's historic structures.
Human rights group Amnesty International has warned of a major humanitarian disaster in the wake of the rebellion.
Meanwhile, Ecowas is preparing a force of up to 3,000 soldiers which could be deployed to stop the rebel advance.
The Tuaregs, who inhabit the Sahara Desert in the north of Mali, as well as several neighbouring countries, have fought several rebellions over the years.
They complain they have been ignored by the authorities in Bamako.