The midfielder had been called up by head coach Zlatko Dalic for Saturday's final Euro 2020 qualifying match against Slovakia, in which a draw will be enough for the World Cup finalists to progress from Group E.
Croatia then meet Georgia in a friendly match next week.
However, Rakitic has gone back to Catalonia due to a heel problem and has not been named in the Barca squad for a charity game against Cartagena, the club confirmed on Tuesday.
He told Novi List in his homeland: "I'm afraid I cannot help the team, but I'm convinced my team-mates will have success without me."
The 31-year-old has struggled for regular football this season, starting just once in LaLiga for Ernesto Valverde's side.
The former Sevilla star has been linked with a possible January move, with Juventus, Inter and AC Milan among the clubs said to be interested.