* Mali been in turmoil since coup in March 2012
* Keita has room to pick own team, free from political debts
* Cisse's camp says will do better in legislative poll (Writes through with details, comment)
By Daniel Flynn and Tiemoko Diallo
BAMAKO, Aug 15 (Reuters) - Ibrahim Boubacar Keita won Mali's presidential runoff with 78 percent of the vote, the government said on Thursday, giving him a strong mandate to seek peace with northern separatists and for sweeping reforms to the army after a military coup.
Sunday's vote marked a transition back to democratic rule after the March 2012 coup plunged Mali into turmoil, allowing Islamist insurgents to seize the desert north. A French-led military intervention in January liberated the region.
Former Prime Minister Keita, whose rival Soumaila Cisse had already admitted defeat on Monday, has said his first priority will be to forge a lasting peace in northern Mali with Tuareg separatist rebels.
Many in the country's populous south, however, are strongly opposed to ceding more autonomy and funds to the northerners, who they blame for the country's current crisis.
Keita also faces huge challenges in reforming the military, tackling widespread corruption and reviving Mali's ailing economy. His hand will be strengthened by 3.25 billion euros ($4.31 billion) in reconstruction aid pledged at a conference in Brussels in May.
"This vote shows that Keita is loved by the people. Now he is the master of his own destiny. He can do what he wants and choose the team that he wants," said Mariam Diallo, a political campaigner and analyst in Bamako. "But he must be careful not to disappoint the people."
General Moussa Sinko Coulibaly, minister for territorial administration, said turnout at Sunday's vote fell slightly to 46 percent from the record level of 49 percent registered in the July 28 first round.
Some 6.8 million Malians were registered to vote.
Keita, who captured the public mood with promises to restore the dignity of the once-proud nation, had received the endorsement of 22 of the 25 losing candidates from the July 28 first round.
Many Malians are now waiting to see if Keita, due to be inaugurated on Sept. 19, will pack the cabinet with his backers to repay political favours, or name a technocratic government many say is needed to push through much-needed reforms.
He has promised zero tolerance for corruption and vowed to avoid the mistakes of ousted President Amadou Toumani Toure, whose unity governments meant there was no criticism of Mali's ineffectual administration, undermining faith in democracy.
A spokesman for Cisse, who pledged on Tuesday to give Mali a real opposition for the first time in years, welcomed the results.
"We will work to improve this score still further in the coming legislative elections to have more members of parliament so we can fully play our role of opposition," Amadou Koita said.
The results need confirmation from the Constitutional Court but this is a formality as Cisse says he will not challenge them.
They come a day after the government of interim President Dioncounda Traore promoted coup leader Captain Amadou Sanogo to the rank of four-star general. The move, criticised by human rights groups, was a step towards Sanogo leaving the army, diplomats said. ($1 = 0.7538 euros) (Writing by David Lewis; Editing by Bate Felix and Alison Williams)