Djukanovic wants to develop the predominantly Orthodox country, a part of which has strong pro-Russia sympathies, by joining the EU.
His Social Democratic Party (DPS) announced victory after the first round of voting and the leading challenger accepted defeat.
Earlier test polling by CEMI, which is tasked with releasing the first results, gave his main rival, Mladen Bojanic, 34.1 per cent.
Bojanic quickly conceded saying, "Montenegro has chosen what it has chosen." Having dominated politics in the former Yugoslav republic for nearly 25 years, Djukanovic stepped down as prime minister in October 2016. He announced his comeback last month.
The 56-year-old is expected to transform the presidency, previously a ceremonial post held by his ally Filip Vujanovic, into the real seat of power in the country of 620,000 people.
Djukanovic was the most high-profile of the seven candidates, with posters plastered all over the capital Podgorica -- where a third of Montenegro's population lives -- proclaiming him as "leader, statesman and president of all citizens".
"I will win today," Djukanovic had said after voting.
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