Colombian media reported after Sunday's finish to the Tour in Paris that the 26-year-old would not feature in the road race after suffering with an illness during the race.
Despite that, Quintana still managed to finish third overall behind Frenchman Romain Bardet (Ag2r La Mondiale) in second and Chris Froome (Team Sky) in first.
He will now reportedly undergo medical tests to determine exactly what he has, with a tilt at the Vuelta a España title on the cards towards the end of August.
Quintana's withdrawal from the Colombian road race squad could see his teammate Winner Anacona called up, although Jarlinson Pantano should be favourite to replace him after a successful Tour de France which saw him claim a stage victory.
One of them will join a formidable line-up for the road race, with Esteban Chaves, Rigoberto Uran, Sergio Henao and Migel Angel Lopez all set to take to the start line in Rio.
Quintana meanwhile, will head back home to reflect on a slightly lacklustre Tour de France, with the Vuelta set to start on August 20.
"I head back home from this Tour full of happiness." Quintana said, "it's a major feat for me to finish on the podium after all difficulties I had to go through in this race.”
“It's obvious that we came into this race with a much bigger and ambitious goal, but we've got many years ahead to keep trying."
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