The 35 year-old is injured and will miss Iran’s games in North Korea, at home to UAE and then in South Korea.
If Iran fail to collect the points necessary to book a place in South Africa, the Persepolis star’s age will count against a return to Team Melli.
Iran have six points from five games and need at least six points to keep World Cup hopes alive.
“Bagheri came several times to the camp and we had a meeting recently. As you know, he is injured and he couldn't train with Persepolis either,” Iran coach Afshin Ghotbi told a press conference in Tehran.
“We have come to conclusion that he won’t be able to play in the next three matches, but his case is still open since he is one of the greatest Iranian players.
"You all know my opinion about Bagheri and he will stay with us if we qualify.”