Louis Michel told reporters in the capital Bamako his team had positively evaluated 98 percent of the 705 polling stations observed yesterday.
He said the "legal framework" for the polls "remains aligned with international standards for democratic elections".
Michel also headed the EU's observation mission for the first round on November 24 and for the presidential polls won by Ibrahim Boubacar Keita in August.
The elections marked Mali's first steps to recovery after it was upended by a military coup last year and then had its northern half occupied by Islamists linked to Al-Qaeda before being then liberated by a French-led military intervention launched in January.
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There were no major incidents during 10 hours of voting but polling stations reported low turnout, with voters scared away by a recent upsurge in rebel attacks against African troops tasked with securing the northern desert alongside French and Malian soldiers.
Preliminary results showed Keita's party, the Rally for Mali, had won "the lion's share" of votes in the second round, according to a member of the government's results collection committee.
Catherine Ashton, the EU's foreign policy chief, called on "all candidates and parties involved to accept the verdict of the ballot box" in a statement released in Brussels.