The second round is a rerun of a 2013 faceoff that Keita won by a landslide over former finance minister Soumaila Cisse.
This year's campaign saw fierce attacks on his failure to dampen a wave of jihadist bloodshed and ethnic violence.
But public enthusiasm has been low and the opposition is fractured.
Keita, 73, was credited with 41.7 percent of the July 29 first-round vote while Cisse, 68, picked up 17.78 percent.
Cisse insisted on Friday he could turn things around on polling day -- warning the status quo would only bring "chaos" in a "torn nation."
But he failed to unite the opposition behind him, and first-round challengers have either backed the president or refused to give voting instructions.
Few Malians attended a string of planned marches and protests called for by opposition leaders in the capital Bamako ahead of the run-off.
As a result, Keita, commonly named "IBK" after his initials, is the clear favourite.
A few hundred Keita supporters gathered late on Friday in the capital of Bamako for the last meeting of the campaign.
"He needs to finish what he started," Silandou Soumare, a civil servant, told AFP. "With all Malians on board, we can have peace in Mali!"
In 2013, Keita won more than three-quarters of the vote.
Peace deal
Voting will be open from 0800 to 1800 GMT. Turnout was low in the first round of voting at around 40 percent.
The first round was peppered by violent attacks and threats from armed groups that led to several hundred polling stations being closed, mainly in the lawless central region.
Security services said Saturday they had disrupted a plot to carry out "targeted attacks" in the capital Bamako on the eve of the runoff.
Three members of a "commando" cell who were planning attacks had been arrested, the security services said in a statement, adding that the trio were also suspected of involvement in a robbery which left three people dead in 2016.
Security will be tightened for the second round, an aide in the prime minister's office said, with 20 percent more soldiers on duty.
This means 36,000 Malian military will be deployed, 6,000 more than two weeks earlier, with a particular focus on the Mopti region in the centre of the country where voting stations had been closed, Cheick Oumar told AFP.
The three main opposition candidates 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's party told AFP in the early hours of Sunday that ballot papers were already circulating, several hours before polls opened.
Outside Mali, the hope is that the winner 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.
Jihadist 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 rooting out jihadists and restoring the authority of the state.
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