Counting is under way in some of the 23,000 polling stations across the West African nation to determine if incumbent Ibrahim Boubacar Keita will remain in office who is challenged by Soumaila Cisse.
Counting is under way in some of the 23,000 polling stations across Mali after voting ended at 1800 GMT even as a polling station chief was killed by suspected militants in the north of the country in a disrupted presidential run-off vote on Sunday.
Security had been drastically boosted ahead of the election's second round between President Ibrahim Boubacar Keita and former finance minister Soumaila Cisse.
But over 100 stations had to be closed in the restive central and northern regions, according to local observer group POCIM.
"Jihadists came this Sunday around 13:30 (1330 GMT) to a polling station in Arkodia," in the northern Timbuktu region, a local official told AFP news agency.
"They asked everyone to put their hands up. The polling station president tried to escape. The jihadists shot and killed him," the source said.
The first round vote on July 29 was marred by violence and threats from armed groups that led to several hundred polling stations being closed – but no casualties had been reported.
Authorities in the vast West African nation said on Saturday they had disrupted a plot to carry out "targeted attacks" in the capital Bamako on the eve of the vote.
Sunday's ballot in Mali is a rerun of a 2013 face-off between Keita, 73, and Cisse, 68, amid a wave of militant bloodshed and ethnic violence.
This year's campaign saw fierce attacks on Keita's perceived failure to halt the violence, as well as mounting accusations of vote fraud.
But public enthusiasm has been low and the opposition is fractured.
"We hope the new president does better and knows how to make up for past mistakes," voter El Hajd Aliou Sow, a retired civil servant, told AFP.
Mali, a landlocked nation home to at least 20 ethnic groups where the majority of people live on less than $2 a day, has battled militant attacks and inter-communal violence for years.
After the first-round vote the pool of candidates was reduced from 24 to two, as Keita was credited with 42 percent of the vote and Cisse picked up 18 percent.
Keita cast his vote in Bamako shortly after 0900 GMT on Sunday and warned against "staged" electoral fraud after accusations of ballot box stuffing and other irregularities.
"How could you stage fraud when you are assured of the support of your people?" Keita said.
Cisse's party told AFP in the early hours of Sunday that ballot papers were already circulating, several hours before polls opened.
The three main opposition candidates had mounted a last-ditch legal challenge to the first-round result, alleging ballot-box stuffing and other irregularities. But their petition was rejected by the Constitutional Court.
Cisse has failed to unite the opposition behind him, and first-round challengers have either backed the president or refused to give voting instructions.
Local observers said voter turnout was low amid heavy rains in several regions, the West Africa Network for Peacebuilding (WANEP) said in a statement.
Polling stations closed
Results are expected within five days.
Turnout was low in the first round at around 40 percent.
Security had been tightened for the second round, an aide in the prime minister's office said, with 20 percent more soldiers on duty.
But voting could not take place in several areas, including the northern village of Kiname, 120 kilometres from Timbuktu, where "armed men came and took all the voting material to the river bank and set it on fire," a resident told AFP.
"There was no voting in Toguerekotia in the Sossobe district because of insecurity," WANEP, which has 150 observers across the country, said in a statement.
Strengthening 2015 accord
Outside Mali, the hope is that the winner of the election will strengthen a 2015 accord that the fragile Sahel state sees as its foundation for peace.
The deal brought together the government, government-allied groups and former Tuareg rebels.
But a state of emergency heads into its fourth year in November.
Militant violence has spread from the north to the centre and south of the vast country and spilled into neighbouring Burkina Faso and Niger, often inflaming communal conflicts.
France still has 4,500 troops deployed alongside the UN's 15,000 peacekeepers and a regional G5 Sahel force, aimed at restoring the authority of the state.