Many expect Former PM Ibrahim Boubacar Keita, who won 40% of the vote in the first round, to defeat ex-Finance Minister Soumaila Cisse.
The election follows more than a year of turmoil which included a coup and a French-led military intervention to oust Islamist rebels from the north.
The victor will oversee more than $4 billion in foreign aid promised to rebuild the West African state.
A 12,600-strong United Nations Stabilisation Mission in Mali (Minusma) is currently deploying, as France begins to withdraw its 3,000 troops.
The UN has stressed the importance of the election to the restoration of constitutional order and the start of national dialogue and reconciliation.
A record 49% of the 6.8 million registered voters cast a ballot in first round on 28 July.
Soumaila Cisse, who was second among the 27 candidates with 19.7% of the vote, complained that there was widespread fraud, with more than 400,000 ballots declared spoiled.
However, Mali’s Constitutional Court rejected the allegations and the head of the EU election observer mission, Louis Michel, praised the electoral process for its transparency.
Ahead of Sunday’s second round, for which some 21,000 polling stations are due to open across Mali at 08:00 GMT, Louis Michel said he had been “positively surprised” by preparations.
Ibrahim Boubacar Keita – who is popularly known by his initials, “IBK” – has urged voters to give him what he called a “clear and clean” majority in the run-off.
“My first priority would be the reconciliation of the country. After the trauma that it has suffered, a new start is needed,” he told reporters on Saturday.
But IBK also said he would be pursuing “a real peace… not a false one”.
Ibrahim Boubacar Keita, 68, has the support of influential moderate Islamic leaders, and 22 of the 25 losing first-round candidates have given him their backing.
Soumaila Cisse, 63, has run on pledges to improve education, create jobs and reform the army. He has been more openly critical of the leaders of last year’s military coup than Ibrahim Boubacar Keita.
“I am confident, because it is not about adding to the votes from the first round, there will be new votes, it is a new election,” he told the AFP news agency on Saturday.
“Everything restarts from zero.”
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