Thousands queued outside polling stations across the country, which saw sporadic outbreaks of violence as the elections approached, including in the capital at the weekend.
Some then cast their ballots while others complained polls were late opening or that they did not know where to vote.
After a last-minute scramble to prepare for the presidential and parliamentary votes, final rallies were cancelled in Kinshasa due to clashes between rival supporters, security forces opened fire on crowds and the main presidential challenger was prevented from campaigning.
The polls - which pit President Joseph Kabila against 10 rivals while more than 18,500 candidates compete for 500 seats in parliament - will test progress towards stability after decades of misrule and two wars in the last 15 years.
Around 5.4 million people were killed by the last war, largely through hunger and disease.
It ended formally in 2003, but localised violence in the mineral-rich state has continued, especially in the east, where a plethora of local and foreign rebel groups vie for control.
Addressing the nation on Sunday evening, Kabila, seen by many as the favourite due to the advantages of incumbency, warned against a return to widespread violence.
"Our country has come a long way, from war and conflict of every type. We must take care not to go back to that," he said.
In the eastern lakeside town of Goma, security was heavy and polls opened slightly late but voters were enthusiastic.
"I am happy to have voted. I want change so I hope those who lose accept the results. We don't want trouble," Joel Mweso, a student, told Reuters.
A Reuters witness also saw residents in the capital, Kinshasa, voting after initial delays. International observers said they had received reports of some delays elsewhere across the nation, but it was too early to give details.
Underscoring security fears, two election commission trucks were ambushed and torched overnight by gunmen just outside Lubumbashi, the usually quiet capital of the mining province of Katanga, the provincial interior minister told Reuters.
Election commission chief Daniel Ngoy Mulunda said Congo would prove critics wrong with credible and peaceful polls.
"Everyone's going to vote tomorrow, it's going to be a celebration of democracy. The Congolese people are going to take the second step in the consolidation of their democracy. We have kept our promise," he said on the eve of the vote.
The first post-war election in 2006 was seen as broadly free and fair but gunbattles erupted after the voting.
United Nations troops and helicopters from Angola and South Africa have been called on to ferry election material to 60,000 polling stations across a nation the size of Western Europe with little infrastructure so some 32 million people can vote.
Provisional results are due on Dec. 6.
Even in the capital voters complained of last-minute confusion over where they were meant to be voting due to polling stations being moved and errors with voter lists.
"We thought voting would be easy, but now we've been told we have to go somewhere else, we don't know where," said voter Bibi Mbao. "We're happy to vote but we're a bit confused, because we're being sent left and right."
The opposition has also protested that election lists were not properly vetted, leading to potential fraud. After outbursts of violence during the campaign, there are also fears of a contested result.
"COME A LONG WAY"
Andre Kimbuta, the governor of Kinshasa province, said some areas of the city were difficult to access and polling stations would only receive ballot papers in the morning. Torrential rain began to fall in parts of the capital by mid-morning.
With more than 1,400 legislative candidates in one Kinshasa constituency, some voters struggled to fit newspaper-sized ballot papers into the clear plastic ballot boxes provided.
A European Union observer mission on Sunday condemned moves by the police on Saturday to prevent Kabila's rival, veteran opposition leader Etienne Tshisekedi, from campaigning.
Kabila came to power when his father Laurent was assassinated in 2001 and then won the 2006 poll.
The failure of the opposition to unite behind a single candidate - after Kabila's camp pushed through a law scrapping the need for a run-off if no candidate secures a majority in the first round of voting - has bolstered his chances.
But Tshisekedi, who has spent decades in opposition and boycotted the last poll due to complaints of fraud, has drawn increasingly large crowds as his campaign, which started late, picked up momentum.
Peter Pham, director of the U.S.-based Michael S. Ansari Africa Center, said it appeared that Tshisekedi had cemented himself as the anti-Kabila vote amid frustrations at the slow pace of progress, even if no formal alliance was in place.
"Ironically, the government's ham-fisted attempts to obstruct his campaign have only served to enhance his stature," he said. (Additional reporting by Kenny Katombe in Goma; writing by David Lewis; editing by Philippa Fletcher)