The second round is a rerun of a 2013 faceoff that Keita, 73, won by a landslide over former finance minister Soumaila Cisse.
This year's campaign saw fierce attacks on Keita's perceived failure to dampen a wave of extremist bloodshed and ethnic violence, as well as mounting accusations of vote fraud, Presstv Reported.
But public enthusiasm has been low and the opposition is fractured.
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 extremist attacks and intercommunal violence for years.
After the July 29 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, 68, picked up 18 percent.
That vote 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 services said Saturday they had disrupted a plot to carry out "targeted attacks" in the capital Bamako on the eve of the runoff.
Several polling stations were again closed in the restive central and northern regions on Sunday due to insecurity.
Voting will close at 1800 GMT and results are expected within five days. Turnout was low in the first round at around 40 percent.
Security has been 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 center of the country where voting stations had been closed.
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.