The unrest cast a pall over the presidential and legislative elections as polls closed at 5:00 pm (1600 GMT) and counting began. Preliminary results in the presidential race are not expected until December 6, while national assembly results are due January 13.
President Joseph Kabila, who has been in power since 2001, is tipped to win a new five-year term running against a divided opposition field of 10 candidates, after parliament changed the constitution in January to scrap two-round elections in favour of a single-round, first-past-the-post system.
Tensions flared early in the day as the flashpoint city of Lubumbashi, capital of the restive mining province of Katanga, erupted into violence with a series of attacks allegedly carried out by separatist rebels.
In the day's worst incident, gunmen opened fire on a polling station in the centre of the south eastern city.
A poll worker said the men shouted, "We have come to liberate you!" before killing two policemen at point blank range and a woman who was hit by a stray bullet.
Armed men in Lubumbashi also launched a pre-dawn attack on a convoy of jeeps carrying election materials.
Officials have said seven or eight attackers were later tracked down and killed by military and police forces. Katanga governor Moise Katundi said the situation in the province was "under control".
An ex-member of a separatist movement fighting for the province's independence told AFP by phone from South Africa that the group had carried out the attack to call for an independence referendum instead of "this vote that doesn't have anything to do with us in Katanga".
WIDESPREAD VIOLENCE ACROSS THE CITIES
In the central town of Kananga, a stronghold for veteran opposition leader Etienne Tshisekedi, voters upset over voting delays and allegations of fraud torched a string of polling stations, stole ballots and blocked a truck from delivering election materials, a UN source said.
In the capital Kinshasa, the day proceeded without major incident until police cars, two armoured vehicles and some 150 riot police blockaded a main road as Tshisekedi, Kabila's main rival, went to cast his ballot.
The run-up to the presidential and parliamentary polls had already been marred by violence pitting Kabila's and Tshisekedi's supporters against each other.
Tshisekedi's supporters also clashed with police on Saturday in Kinshasa as officials banned candidates from holding their final rallies after violent clashes lead to the death of at least two people.
OTHER ELECTION DIFFICULTIES
Logistical headaches in organising the vote in a nation two-thirds the size of Western Europe, with a roads network that is crumbling and limited after seven years of war and decades of under-development, had raised fears the polls could be postponed.
The elections are just the second since back-to-back wars from 1996 to 2003 in a country that remains one of the world's poorest despite its abundance of cobalt, copper, diamonds and gold.
Voters interviewed at polling stations voiced frustration with their poverty. Two-thirds of the country's 67.8 million people live on less than $1.25 a day.
