Thousands of people died at the hands of paramilitary groups during the country's bloody civil war against rebel groups, most notably the Revolutionary Armed Forces of Colombia (Farc).
Earlier, the president acknowledged in a statement that the arrest "hurts me", but he said it was "a pain I will accept with patriotism and
without avoiding the fulfilment of my responsibilities".
More than 60 politicians, many from political parties allied to the president, are under investigation for suspected ties to armed groups.
At least 32 of those are in jail while prosecutors examine their ties to the militias.
Uribe, a former congressional leader, was sought on charges that he struck deals with former paramilitary commanders, the attorney-general's office said in a statement.
"Uribe is being investigated for a meeting he had with former paramilitary commander Salvatore Mancuso before the elections of March 10, 2002 and with Jairo Castillo Peralta, alias "Pitirri", in November 1998," it said.
Uribe has denied the allegations, describing Castillo as "a liar, an extortionist, a killer and a bandit".