The bodies, found on Thursday, were those of reporter Javier Ortega, 32, photographer Paul Rivas, 45, and their driver Efrain Segarra 60. The trio was abducted on March 26.
The bodies "will be handed over to Ecuadoran authorities who already have arranged the air transport from Cali," a Colombian government statement said.
The trio, who worked for Ecuador's influential El Comercio newspaper, were kidnapped while covering a story on violence along the remote border, prompting both countries to send troops to hunt down the perpetrators.
Authorities blame the kidnapping on a gang led by Walter Patricio Artizala, better known as "Guacho," a former Colombian guerrilla with the now-defunct FARC.
Ecuador's northeastern border region is covered with dense jungle and crisscrossed by rivers leading into the Pacific, has become a paradise for drug traffickers.
The case has strained ties between Ecuador and Colombia.
Ecuador's Foreign Minister Jose Valencia said the bodies would be returned on Wednesday afternoon on an Ecuadoran air force flight.
There was no immediate identification of a fourth body found in the same grave.
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