The opposition Liberal Party won 18 senate seats.
The congressional election, which got under way on Sunday, is considered a key barometer of how Colombians will vote in the May 30 presidential contest.
After two terms in office Uribe's nurturing of the economy to its best performance in 30 years and his crackdown on the Revolutionary Armed Forces of Colombia (Farc), have earned him a near 70 per cent popularity rating.
But a court decision last month barred him from seeking a third consecutive term as president and his term will end in August.
Despite Uribe's popularity, both chambers of congress have been unable to shake off their association with scandal.
Twelve pro-Uribe legislators have been convicted on charges linked to rightist paramilitary death squads, while at least another 80 legislators are under investigation for alleged links to paramilitary groups.
Security was tight for the vote, with about 150,000 military and police deployed across Colombia to safeguard some 77,000 polling stations.
Al Jazeera's Teresa Bo, reporting from a polling station in Corinto, said there had been reports of intimidation by a paramilitary group on the election day.
"[Reports] are suggesting that paramilitaries have been forcing people, especially in rural areas, by telling them which candidate they have to go for," she said.
"Let us not forget that many paramilitary groups are trying to get candidates into congress."
One political party was struck from the voting list on suspicion its leaders had links to paramilitaries, though opposition groups claim the party simply renamed itself and kept the same people, or their relatives, in charge.
About 29.8 million Colombians were registered to vote to choose from 2,539 candidates to fill congress' combined 268 seats.