Former Prime Minister Ibrahim Boubacar Keita won Mali's presidential election, after his opponent Soumalia Cisse conceded defeat late on Monday, avoiding a protracted legal battle over the outcome.

"My family and I went to congratulate Mr. Keita, the future president of Mali, on his victory. May God? bless Mali," Cisse, a former finance minister, said via Twitter.

In the first round vote, Cisse had accused Keita of electoral fraud and filed a complaint with Mali's highest court. But Cisse ultimately lost that case. Keita had been widely expected to win the election, after pulling in nearly 40 percent of the vote in the first round.

"This election made a positive impression on me, it went off calmly and peacefully," said Annette Lohmann, head of the Malian branch of the Friedrich Ebert Foundation, a German think tank, in the capital Bamako.

Turnout hindered by bad weather?

Some observers blame the weather for the poor turnout. There was heavy rain on the morning of election day, which made the journey to polling stations across Mali's difficult terrain especially troublesome. But Christopher Fomunyoh from the National Democratic Institute, an American NGO, said the weather wasn't the only reason Malians were reluctant to go out and vote.

"A number of them were backing candidates that didn't make it through to the run-off. Those voters preferred to stay at home, rather than opt for another candidate," Fomunyoh told DW from Bamako. But he said the run-off was better organized than the first round. Two weeks ago, a number of Malians didn't know where they should be casting their ballots. This time they were able to reach the right polling station more quickly.

These presidential elections are considered crucial for Mali's future. It was the first time people have gone to the polls since the coup on March 22, 2012, and the occupation of the north of the country by Islamists and the separatist National Movement for the Liberation of Azawad (MNLA). The attacks with which Islamists had threatened to disrupt the election failed to materialize. Thousands of African and French soldiers were on duty on election day to ensure voter safety.

Formidable challenges ahead

Even though the election appears to have gone off smoothly, it was not perfect. "Not everybody who could have voted was registered in time," said Lohmann. "Almost no refugees were able to cast their ballots." She was referring to some 200,000 Malians who, according to United Nations sources, fled to Burkina Faso, Niger, Mauretania and Algeria in order to escape the fighting at home.

The challenges Keita faces are formidable. The economy contracted last year by 1.2 percent, the infrastructure in the north has been destroyed by war, and peace with the rebels remains fragile.