With 85% of ballots counted, the conservative president scored a stronger than expected 62% of the vote - surpassing the 50% needed to win outright in the first round.
Uribe's victory marks the first time in more than a century that an incumbent Colombian leader has been elected to a second term.
Carlos Gaviria of the left-leaning Alternative Democratic Pole party was second with just over 22% of the votes counted in the partial results.
"There are many complaints, some concerns in certain sectors, but the priority at this stage is the triumph of President Uribe," Gaviria told Radio Caracol.
The election was the most peaceful in years in a country that has seen four decades of conflict between the government, Marxist rebels, right-wing paramilitaries and drug-traffickers.
About 220,000 Colombian soldiers were on duty at polling stations during the day's voting.
In the capital Bogota, tanks patrolled the streets and heavily armed combat troops frisked motorists at random checkpoints.
Colombian security forces said they killed 12 Revolutionary Armed Forces of Colombia (Farc) members - in clashes on Saturday.
The victory gives Uribe the second four-year term he says he needs to win the battle against rebels and the drug trade they often control.
Opponents accuse the president of focusing his war on Colombia's left-wing rebels and their ties to drug-trafficking, while allowing the country's murderous far-right paramilitaries to grow into a political force.