In accepting the fines, the prosecution agreed not to name or prosecute the executives involved in ordering the payment of protection money.
The US justice department said in March that Chiquita's payments to the paramilitaries "were reviewed and approved by senior executives of the corporation, to include high-ranking officers, directors and employees".
Chiquita, which sold its Colombian subsidiary Banadex in June 2004 for about $43.5m, has previously said that the payments were made to protect employees in a violent region.
The company still faces a civil lawsuit brought in July by the families of 173 people who died in violent incidents across Colombia.
The complaint, filed in a New Jersey district court, accuses Chiquita Brands International of funding and arming known terrorist organisations in order to maintain control of Colombia's banana growing regions.
The suit seeks unspecified damages, but could potentially cost tens of millions of dollars if it results in damages being awarded to each victim of any group paid by Chiquita.
Colombia's paramilitary groups were organised as private armies in the 1980s, ostensibly to protect landholders from left-wing fighters who were extorting "war taxes".
The AUC has since been accused of killing civilians and of drug trafficking.
The group began a process of disarmament in 2003.
Chiquita has also acknowledged making similar payments to Colombia's main left-wing rebel groups.