"To carry out an exhaustive evaluation of bilateral relations, (the government) has recalled its ambassador from Bogota," the foreign ministry said in a statement.
Colombia said it would keep its envoy in Caracas, the first time in days one side has reacted to a move by the other without further escalating the dispute between Andean neighbours with $6bn in annual trade.
"We are going to keep monitoring this situation to see what happens," Fernando Araujo, Colombia's foreign minister, said.
On Sunday, Chavez, an anti-American socialist, said he had frozen relations with Colombia, accused Uribe of lying in the dispute, and said the spat could affect cross-border business.
Uribe, a close Washington ally, responded by accusing Chavez of favouring the FARC, which is waging Latin America's longest-running rebel insurgency despite security improvements.
Chavez's clash with Uribe is his second diplomatic dispute this month. He has frozen ties with Spain after its king told him in public to "shut up".
Chavez also faces this Sunday his toughest vote battle since taking office in 1999 in a referendum on letting him run for re-election indefinitely, with polls showing that he may lose.