Ramirez was not involved in Colombia's 3-0 friendly win over Jordan in Buenos Aires on Friday, and coach Jose Pekerman confirmed the 33-year-old would not be fit for their Brazil campaign.
The Morelia man has not played a competitive game since appearing in a Liga MX match in late April.
Ramirez tweeted his disappointment at being ruled out of what loomed to be his only chance to play at a World Cup.
"It is great sadness, but the support of each of you fills me with messages of strength. Thank you to everyone," Ramirez tweeted.
Colombia can replace Ramirez in the squad, but must reveal their inclusion more than 24 hours prior to their opening clash.
The South Americans open their World Cup campaign against Greece on June 14.
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