Figures for Sunday's ballot announced on live television showed former prime minister Ibrahim Boubacar Keita in the lead with 39.2% of the vote, ahead of main rival Soumaila Cisse with 19.4%.
The election is seen as key to Mali's recovery after a coup in March last year overthrew Amadou Toumani Toure, plunging one of the region's most stable democracies into political crisis and leading to a radical Islamist insurgency.
As hardline al-Qaeda allies took control of the country's vast desert north, and threatened to extend their often violent rule, former colonial power France launched a military offensive in January to drive out the radical Islamist fighters.
"The new Mali is being built with patience, calm and serenity for all Malians united around these challenges above ambitions and pretensions, and not in a climate of agitation and invective … "
Keita tweeted in his latest campaign update ahead of the announcement.
Four former prime ministers and an array of political heavyweights – but just one woman – featured in a list of 27 presidential hopefuls, although analysts always characterised the election as a two-horse race between Keita and Cisse.
Dramane Dembele, the candidate for Mali's largest political party, the Alliance for Democracy in Mali, polled just 9.6%, taking third place.
The result will be seen as something of a surprise after Keita took a comfortable early lead over Cisse, a former finance minister and erstwhile chairperson of the Commission of the West African Economic and Monetary Union.
Interior Minister Moussa Sinko Coulibaly, who announced the result, had said there would be no need for a second round if the trend continued.
Cisse's party said Wednesday the election had been marred by "ballot stuffing", a form of electoral fraud in which people submit multiple ballots during a vote in which only one ballot per person is allowed.
Acting president Dioncounda Traore and United Nations secretary general Ban Ki-moon have acknowledged that the vote may be "imperfect" in a country with 500 000 citizens displaced by conflict, but have urged Malians to respect the outcome.
Critics have argued that Mali, under pressure from the international community, rushed to the polls and risked a botched election which could do more harm than good.
But initial estimates put the turnout above 50%, a huge improvement on the 36% who voted in 2007, and Mali was praised by the international community for running a transparent, credible and peaceful election.
Despite heavy security during voting after the Movement for Oneness and Jihad in West Africa – one of the main armed groups in northern Mali – said it would "strike" polling stations, no serious incidents were reported on election day.
A UN peacekeeping mission integrating more than 6 000 west African soldiers into its ranks is charged with ensuring security in the post-election period, and will grow to 11 200 troops, plus 1 400 police, by the end of the year.
The deployment allows France to start withdrawing most of the 4 500 troops it sent to Mali in January to stop the radical Islamists from advancing towards Bamako and Paris plans to have just 1 000 troops on the ground before the end of the year. – AFP