Malis ousted former president
Toure flew into the capital, Bamako, the scene of his downfall on March 22, 2012, when mutinous soldiers overthrew the government and detained him.
The coup led by army captain Amadou Sanogo toppled what had been heralded as one of the region's most stable democracies, before the country's northern territory was overrun by Islamist rebels allied with Al-Qaeda.
Toure, who arrived with his family on board the presidential plane, travelled to the personal residence of President Ibrahim Boubacar Keita, with whom he is due to have lunch.
He was welcomed by the prime minister and security minister, along with hundreds of supporters at around midday (1200 GMT).
Keita said on Friday the moment had arrived "for us to tell our brother Amadou Toumani Toure to return to Mali," while Toure told AFP from the Senegal capital, Dakar, that he was "not there to do politics".
Toure has been living in exile in Senegal ever since he was deposed.
He was accused by Keita's government in 2012 of treason over the failure of soldiers to tackle a rebellion led by Tuareg people that eventually led to jihadists trying to take over the country. The charges were dropped last year.
Islamist militants took control of northern cities in Mali in March and April 2012 but were chased out by a French-led military operation launched in January 2013, which is still under way.
Mali's army, French soldiers and a UN mission (MINUSMA) have little control of large tracts of the country, which regularly come under attack in spite of a peace accord signed with Tuareg leaders in May and June 2015, aimed at isolating the jihadists.