The polls mark the troubled west African nation's first steps to recovery after it was upended by a military coup in March last year, finalising a process begun with the election of President Ibrahim Boubacar Keita in August.
"This second round establishes the recovery on a foundation of legitimacy in this country. It will give us more strength, more power to say 'Mali' and that's what Mali needs," Keita said after casting his ballot in the capital Bamako.
Turnout looked low however in Bamako, sparking fears that voters would be scared away by a recent upsurge in violence by Al-Qaeda-linked rebels against African troops tasked with election security alongside French troops and the Malian army.
Two Senegalese UN peacekeepers were killed and seven wounded last day when a suicide bomber ploughed his explosives-laden car into a bank they were guarding in the northeastern rebel bastion of Kidal.
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The French army has been carrying out an operation against Al-Qaeda in the Islamic Maghreb (AQIM) north of the desert caravan town Timbuktu over the past week, killing 19 militants, according to French Foreign Minister Laurent Fabius.
In the first round of the election on November 24 just 19 of the national assembly's 147 seats were allocated, with turnout at 38.6 per cent, a drop of almost 13 percentage points from the first round of the presidential vote.