Sunday's second round is likely to return Ibrahim Boubacar Keita to the helm of Mali despite fierce criticism of his handling of the country's fight against jihadist violence and ethnic attacks.
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The first round, held last month, was peppered by violence and threats from armed groups that led to several hundred polling stations being closed, mainly in the lawless central region.
Security will be tightened for the second round, an aide in the prime minister's office said on Saturday, 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.
Security forces in Bamako said Saturday they had arrested three members of a "commando" cell who were planning attacks in the capital this weekend.
The three men, suspected of involvement in a robbery which left three people dead in 2016, are accused of "plotting targeted attacks" over the weekend, the security services said in a statement.
"They were in the planning stage," it said. "We are not currently going to provide too many details in terms of arms and munitions seized, but obviously during the election period it's better to have them arrested than still at large."
'Torn nation'
Sunday's vote is a rerun of a 2013 faceoff that Keita won by a landslide over former finance minister Soumaila Cisse.
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 clear favourite.
The three main opposition candidates mounted a last-ditch legal challenge, alleging ballot-box stuffing and other irregularities. But their petition was rejected by the Constitutional Court.
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.
Voting will be open from 0800 to 1800 GMT. Turnout was low in the first round of voting at around 40 percent.
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