Despite the historic nature of the polls, voter turnout in the tiny Balkan state of just 650,000 people was lower than expected, with none of the passion and excitement that saw 85 percent of registered voters cast ballots in the independence referendum in May.
Mr Djukanovic's ruling coalition was tipped to win the election, riding a wave of goodwill that followed the proclamation of independence from Serbia on June 3 and Montenegro's prompt acceptance as the newest member of the United Nations.
"I expect these polls to be democratic and enable the election of a government able to respond to the demands Montenegro is facing," the prime minister told reporters after casting his ballot.
The architect of the country's independence drive, Mr Djukanovic campaigned hard on the issue of fast-track integration into the European Union, pushing for an association and stabilisation agreement to be signed by the end of this year as a first step towards joining the 25-member bloc.
Andjela Babovic, a 32-year old chemist, said she had no doubt where her vote was going.
"You have nobody else to vote for but Djukanovic. Although he has been in power for so long, he is still the best and I do not want him to change," she said.
The latest opinion polls had shown support for the ruling coalition running at about 43 percent.
The main opposition bloc led by the pro-Serbian Socialist People's Party of Predrag Bulatovic was expected to win 18 percent of the vote, while a new political force, the Movement for Change -- a non-governmental organisation-turned-party -- was polling at 16 percent, surveys showed.
"This ruling coalition should go into opposition and enable democratic process finally to begin in Montenegro," said the Movement's leader Nebojsa Medojevic.
But many voters seemed unwilling to embrace the prospect of a change of government at such a crucial juncture, especially given divisions within the opposition, who have been unable to focus their attention on much-needed social, economic or political reforms.
"The opposition is only criticising Djukanovic. They offer no program," said Maja Perovic, an unemployed clerk.
"They just want to take over his place, but have nothing to promise for the economy or politics," she said.
Early figures confirmed that turnout was significantly lower than for the May referendum when Montenegrins had queued from the early hours in order to secure their chance to vote.
Only four hours before the polls were due to close at 9:00 pm (1900 GMT), just 49.3 percent of the country's 485,000 eligible voters had cast their ballots for the 81-seat parliament.
Voting day was calm but on the eve of the election police arrested 14 people in ethnic Albanian-dominated south-eastern Montenegro on suspicion of planning terrorist acts.
Two ethnic Albanian parties protested the police action, saying it was "politically motivated" and aimed at putting a pressure on their supporters ahead of the polls.
But the authorities denied such charges, with Mr Djukanovic saying that the police "have professionally and efficiently done their job."
"Life does not halt in the days before the elections. Thieves steal on these days, murderers kill... and those ready to execute terrorist actions are preparing for that," he told reporters.
Alongside the general election, voters were also choosing representatives for their local assemblies and mayors in 14 towns and municipalities throughout the country.
First estimates were expected two hours after closing of the polls.