The 25-year-old was one of 25 players invited by Chris Hughton for the game, which is set to take place on Thursday at the Baba Yara Stadium in Kumasi.
However, despite reporting to camp earlier this week, it was detected that the player was carrying an injury that he sustained against Anderlecht last Sunday.
A statement from the Ghana Football Association (GFA) said Paintsil has been granted permission to travel back to Belgium to start his recovery.
“The Technical team of the Black Stars has granted Joseph Painstil permission to return to his club in Belgium due to injury,” the GFA said.
“The winger sustained the injury in the last period of his League game against Anderlecht on Sunday and was later substituted - forcing him to withdraw from Thursday's Africa Cup of Nations qualifier against Central African Republic.
“The player will return to his club immediately to commence rehabilitation. That leaves Chris Hughton with 24 players to prepare for the match on Thursday.”
Meanwhile, Hughton should have enough cover on the flanks, with Ernest Nuamah, Osman Bukari, Inaki Williams and Jordan Ayew all perfect fits for the role.
The Black Stars need at least a draw against CAR to book their place at next year’s AFCON in the Ivory Coast.