The court´s president, Mauricio González, said that the agreement, signed in June 2009, is not an extension of military pacts dating back from 1952, which he noted did not include giving the US military access to the bases.
The agreement would also grant immunity to US personnel, including 800 soldiers and 600 contractors, and allow C-17 planes to carry heavy equipment and troops.
President Juan Manuel Santos will have to send the agreement to Congress for approval.
The court issued its ruling in response to a case brought by the José Alvear Restrepo Collective, a nongovernmental human rights organization, which sought for the agreement to be declared unconstitutional.
In a statement, Defense Minister Rodrigo Rivera said the government would respect the ruling and suspend the agreement and also study it with regard to international law and existing military cooperation agreements.
The ruling did not bar US military personnel from working on Colombian installations under previous agreements. The United States has given the country around US$1.2 billion a year since 2000 under the sweeping Plan Colombia initiative.
The agreement was harshly criticized by other Latin American nations who considered it a threat to regional security.