President Uribe immediately used his renewed political strength to urge leftist guerrillas to revive the stalled peace process.
The legislative vote was a major setback for the opposition Liberal Party which has ceased to control of the largest congressional faction for the first time.
"I ask the Revolutionary Armed Forces of Colombia to revise its behaviour, review the democratic calling of all Colombians and consider the possibility of serious and urgent peace talks," Mr Uribe said.
The FARC, with 18,000 fighters, is the largest and best-equipped insurgent force in Colombia.
The rebels have stepped up their attacks to defend their influence in rural areas ahead of the elections.
With 80 percent of votes counted, a seven-party ruling coalition appears to have won at least 61 out of 102 senate seats.
Turnout was less than 50 percent, however the voting passed peacefully amid tight security.
Ballot boxes in one are and polling booths in another were burned, and in some of the more remote rural regions, voters were prevented from getting to polling stations.
On Sunday, Mr Uribe urged voters not to be intimidated, as he cast his ballot in Bogota.
"Voting is the best reply that we Colombians have to the violence," the conservative president said.
Around 26.5 million qualified voters selected 102 members to the senate out of 823 candidates and 165 members to the House of Representatives out of 1,968 hopefuls.
The elections were overseen by around 50 international monitors from 15 countries.