The Juventus forward initially tested positive on October 13 while on international duty with Portugal and has since been in quarantine at his home in Turin.
Ronaldo took a PCR test on Tuesday in a late bid to play in the Group G showdown with Barcelona on Wednesday night but, despite continuing to be asymptomatic, it came back positive.
The five-time Ballon d’Or winner said in an Instagram post that he was “feeling good and healthy”.
The 35-year-old then posted a comment saying: “PCR IS B*******,” before appearing to delete the post.
Ronaldo’s absence has prevented the highly-anticipated latest instalment of his rivalry with Lionel Messi.