The photo, which was on the front page of the newspaper Thursday, shows a man in hospital with a tube in his mouth, with the headline "the secret of Chavez's illness," the BBC reported.
Chavez has not been seen in public since he underwent treatment for cancer in Cuba last month.
El Pais, which has collected a number of the first edition of the newspaper and removed the story from its website, said it obtained the image from a news agency, but did not say which one.
The paper has now opened an investigation into "the mistakes that may have been committed in the verification of the photograph".
2014: The Year in Music [PHOTOS]