A statement by the Colombian football federation states that “In the past days, the midfielder underwent medical exams that determined that he is not at the optimum level of competition and so he will not join coach Reinaldo Rueda’s squad,” a statement said.
The statement did not specify what the problem was, but the Everton player has missed several games this season with a calf injury.
Colombia face Qatar 2022 qualifiers away in Peru on 3 June and at home to Argentina five days later.
The Copa America then kicks off on 13 June.
Colombia were meant to co-host the tournament with Argentina but civil unrest there prompted the South American Football Confederation to remove them as joint hosts.
No decision has been taken on where to play the 15 games that were scheduled for Colombia.