Malians Vote in Presidential Runoff
Keita, 73, took 42 percent of the vote in a field of 24 candidates in the first round of voting, compared to 18 percent for the 68-year-old Cisse, who also lost the 2013 election to Keita.
The earlier round of voting was marred by armed attacks blamed on jihadists, including some linked to al-Qaida and Islamic State, and ethnic violence that closed several hundred voting places.
The government stepped up security for Sunday's run-off, deploying an additional 6,000 troops in addition to the 30,000 who already were on duty.
Security services said Saturday they had disrupted a plot to to launch "targeted attacks" in the capital Bamako hours before voting started.
Light turnout was reported as polls opened on a rainy day, but no major terrorist incidents. However, several polling stations were again closed in the capital and northern regions because of a lack of security.
In the northern village of Kiname, one resident told Agence France-Presse that "armed men came and took all the voting material to the river bank and set it on fire."
The election observer West Africa Network for Peacebuilding said there was "no voting in Toguerekotia in the Sossobe district [of the central Mopti region] because of insecurity."
Keita voted in the capital, later telling cheering supporters, "I pledge that all the difficulties we faced are now behind us."
Cisse accused Keita's government of fraud in the first round of voting, but the constitutional court upheld the result.