"I am leaving," Maria Araujo said on Monday.
"I see clearly that the judicial process must be free of any interference."
Uribe has received millions of dollars in US aid to fight drug traffickers and left-wing guerrillas.
Arrest warrants have been issued for at least nine pro-Uribe congressmen since late last year when the scandal first broke out.
One active army colonel has been suspended from his command while he is probed for paramilitary links.
More than 31,000 right-wing armed fighters have demobilised under a peace deal with Uribe's government.
But human-rights groups say powerful paramilitary bosses have been allowed to keep their criminal networks intact.