Maria Araujo, stood down on Monday after her brother Alvaro Araujo, a senator, was jailed last week on charges of collusion with illegal paramilitaries and orchestrating the kidnapping of a political rival.
"The resignation of the foreign minister and the recent arrests of members of the Colombian Congress are positive, though overdue, steps but they leave many questions unanswered"
Patrick Leahy, chairman of the senate subcommittee that controls aid to Colombia
Colombia's supreme court also recommended that prosecutors investigate her father for similar crimes.
Eight Uribe-allied federal politicians have now been jailed for allegedly benefitting at the ballot box from collusion with paramilitaries.
Paramilitaries are responsible for some of the worst massacres in Colombia's five-decade civil conflict, land theft and much of the country's cocaine trade.
The alleged ties between Uribe's political backers and the paramilitaries, has complicated the president's international appeals for help to fight rebels and drug traffickers and modernise the judicial system.
Uribe is counting on billions of dollars in aid from the US and the EU.
Some US Democrats are now calling for $700m in mostly military aid that Colombia gets each year to be reconsidered.
Patrick Leahy, chairman of the senate subcommittee that controls aid to Colombia, in a statement said: "The resignation of the foreign minister and the recent arrests of members of the Colombian Congress are positive, though overdue, steps, but they leave many questions unanswered.
"American taxpayers deserve assurances that the Colombian government has severed links to these terrorist groups."
The EU's delegation in Bogota declined to comment on Araujo's resignation.