The elections have been closely watched abroad, as Mali is a linchpin state in the jihadist insurgency raging in the Sahel.
Keita, 73, picked up 67.17 percent of the vote on Sunday against 32.83 for opposition challenger and former finance minister Soumaila Cisse, 68, who also ran against Keita in 2013, the government announced. Turnout was low, at 34.5%.
Cisse's party angrily vowed to use contest the results, but using "all democratic means."
Mali, a landlocked nation home to at least 20 ethnic groups where most people live on less than $2 (1.76 euros) a day, has been battling a years-long Islamic revolt that has now fuelled intercommunal violence.
Hundreds of people have died this year alone, most of them in Mopti, an ethnic mosaic in central Mali, in violence involving the Fulani nomadic herder community and Bambara and Dogon farmers.
Keita's response to the burgeoning crisis was the big campaign issue, with opposition candidates rounding on him for alleged incompetence or indifference.
But the verbal assaults failed to dent his core support, and a fractured opposition and widespread voter apathy left him firm favourite in the final round.
Voting was also marred by jihadist attacks that forced the closure of a small percentage of polling stations, and by allegations of ballot-box stuffing and other irregularities.
The three main opposition candidates mounted a legal challenge to the first-round result, but their bid was rejected by the Constitutional Court.
'Fraud' claim
Cisse on Monday declared in advance that he would reject the results.
He called on "all Malians to rise up... We will not accept the dictatorship of fraud" -- a verbal broadside that triggered a UN appeal for calm.
On Thursday, as Keita supporters rejoiced, Cisse's campaign chief Tiebile Drame lashed the results as bogus.
"These are their results. They do not reflect the truth of the polls," Drame said.
"We strongly call for people to mobilise," he said, adding however that the party intended to harness "all democratic means" to contest the outcome.
Keita plans to appeal to the Constitutional Court "to get the fraudulent results cancelled" in some regions, Drame said.
Observer missions sent by the European Union and the African Union (AU) have issued provisional reports saying the election was not badly impaired.
"Our observers did not see fraud but irregularities," EU mission chief Cecile Kyenge said. The AU said voting was conducted "in acceptable conditions."
Political analyst Souleymane Drabo downplayed the risk of voter unrest, saying the country's politicians, including Cisse and Keita in past ballots, had a long history "of calling fraud at election time."
"Everyone knows that the page has turned," Drabo said, adding that the most immediate issue for most people was to prepare for Tabaski, the west African name for the upcoming Islamic festival of Eid-al Adha.
But Jonathan Sears, Sahel researcher at Centre Francopaix in Montreal, was more cautious, fearing that doubts about voting transparency could erode Mali's democracy.
"These elections have been a lost opportunity and Cisse's insistence in interrogating the results underlines that," he told AFP. "The rejection is deeply concerning -- if Cisse is speaking for many people, there is a possibility of it being socially disruptive."
Challenges
Keita will take office on September 4, facing high expectations to boost a 2015 peace accord between the government, government-allied groups and former Tuareg rebels.
The credibility of the deal -- billed by Keita as the cornerstone of peace -- has been battered by a state of emergency that heads into its fourth year in November.
France, which intervened to root out jihadists in northern Mali in 2013, still has 4,500 troops in the country.
They are deployed alongside the UN's 15,000 peacekeepers and a regional G5 Sahel force, aimed at fighting the insurgents and restoring the authority of the state in the lawless north.
Another challenge for Keita is to shore up the economy. Income per capita has fallen since 2014, according to the World Bank, and nearly half of the 18 million population live in poverty.
(AFP)