The 27-year-old ruptured the anterior cruciate ligament of his left knee. The Boca Juniors player had won five caps for the national side.
A replacement would be named within hours, Colombia said in a short statement.
The South Americans kick off their World Cup campaign against Japan on June 19, before also playing Poland and Senegal in Group H.
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(Reporting by Andrew Downie; editing by Clare Fallon)
