According to provisional results, Keita secured 39.24 percent of the vote in the July 28 poll, well ahead of Cisse on 19.44 percent, said Moussa Sinko Coulibaly, minister of territorial administration.
Mali’s Constitutional Court must confirm the provisional results before the second round vote can go ahead on August 11.
The announcement of a run-off should ease tensions that have risen since Tuesday when partial results gave Keita a large lead, putting him on track for an outright victory in one round.
Cisse said he would reject the election result if there were no second round of voting.
A record 51.54 percent of registered voters took part in the high-stakes ballot, which is meant to give the West African nation a fresh start after 18 months of political turmoil and war.
Turnout in Mali’s previous elections had never hit the 40 percent mark.