With almost all the ballots counted, Igor Dodon, who wants to restore close ties with Russia, had 52.37% of the vote, while pro-European candidate Maia Sandu, polled 47.63%.
The national vote marks the first direct presidential election in Moldova since 1996.
Since 1996, Moldova’s president has been chosen by parliament.
The election was seen as a battle between those supporting closer ties with Russia and those wanting integration with the EU.
Speaking shortly after the closure of polling stations on November 13, Igor Dodon called on Maia Sandu to preserve public order and abstain from protests.
Igor Dodon, 41, was a deputy prime minister in the Party of Communists government before 2009. He blames widespread corruption in Moldova on the pro-EU parties that have ruled the country since then.
Both candidates criticized the vote as badly organized, highlighting the shortage of ballot papers for overseas voters.
The final voter turnout was 53.3%.
Moldova, a former Soviet republic with has close historical ties with Moscow, declared independence after the break-up of the Soviet Union in 1991.
The country also has a breakaway region supported by Russia, Trans-Dniester.
Moldova has moved to forge closer ties with the EU in recent years, a course championed by Maia Sandu.
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