Counting has started in some of the 23,000 polling stations which closed at 1800 GMT. First results are expected within 48 hours and the official outcome is set to follow on Friday at the latest.
Despite the deployment of 30,000 security personnel throughout the country, several incidents were reported in the north and centre.
According to figures released by the Ministry of Territorial Administration , violence prevented voting from taking place at 644 polling stations (almost 14% of the total). Some stations were set on fire, while numerous instances of violence against election officials were reported.
President Ibrahim Boubacar Keita 73, leads a crowded field of 24 candidates -- including one woman -- bidding for re-election to the post he has held since 2013. He voted in Sebenicoro, near the capital Bamako, surrounded by journalists and supporters.
Keita's record on security has been a dominant theme, with opponents, including several former ministers, accusing him of incompetence.
The international community hopes the poll will strengthen a 2015 accord that Mali, a linchpin state in the troubled Sahel region, sees as the cornerstone for peace.
On the campaign trail, Keita -- commonly known by his initials IBK -- highlighted the achievements of the peace agreement between the government, government-allied groups and Tuareg former rebels to fight jihadist fighters in the country's north.
Armed groups severely disrupted voting in central Mali's Mopti region. In Fatoma village, voting was halted after election officials were assaulted, according to Malian observers and the regional governor.
Violence also struck the village of Gandamia, further east, where polling stations were destroyed and staff were attacked, the sources said.
Violence also marred the lead-up to the vote, despite the presence of 15,000 UN peacekeepers and 4,500 French troops and a heralded five-nation anti-terror G5 Sahel force. A state of emergency will enter its fourth year in November.
More than 300 civilians have died in ethnic clashes this year, according to UN figures and an AFP toll.
Many deaths have occurred in the Mopti region involving the Fulani nomadic herder community and Bambara and Dogon farmers.
Violence, meanwhile, has spread from northern Mali to the centre and south of the country and spilled over into neighbouring Burkina Faso and Niger, often inflaming communal conflicts.
The main al Qaeda-linked terrorist alliance made its presence felt on the final day of campaigning Friday, dubbing the election a "mirage" that would do nothing for the Malian people.
In Mali's north, where the state is barely present, armed groups who signed the peace accord helped to ensure security.
