The Ministry of Territorial Administration on Thursday declared Keita the winner of the repeat poll held on Sunday with 67 percent of ballots cast.
Cisse, a former finance minister, who also ran against Keita in 2013, secured 32 percent of the votes.
Keita will serve his second five-year term as Malian leader.
Cisse had accused the incumbent’s camp of cheating in the first round, which saw him secure 18 percent of the vote against Keita’s 41 percent.
The repeat poll was marred by a low turnout amid security concerns and voter apathy.
Threats by armed fighters forced nearly 500 polling stations – about two percent of the total – to stay closed during the runoff, the government said. One election official was killed in northern Niafunke, in the Timbuktu region.
Keita, who is 73, will take office on September 4. His immediate challenges include strengthening a 2015 peace accord between the government, its allies, and former Tuareg rebels.
The peace agreement raised hopes of stability, but its meaningful implementation has been challenging.
Mali is a landlocked nation home to at least 20 ethnic groups where the majority of people live on less than $2 a day.
The country has battled attacks by armed groups and intercommunal violence for years.