The Chelsea player hurt his knee against West Ham on Sunday, and England's medical staff ruled he would not be able to play after assessing the injury.
However, he remains with the England squad in the hope he will be fit for next Tuesday's match against Montenegro in Podgorica.
Steven Taylor of Newcastle has been called up as cover for the San Marino game.
Hodgson has already lost Rio Ferdinand, who pulled out of the squad on Monday due to his "detailed pre-planned training and medical programme" to manage his body between games.
Chelsea captain John Terry retired from international football in 2012 after the FA charged him with the racial abuse of Rio Ferdinand's brother Anton.
Steven Caulker of Tottenham was called up on Monday to replace Ferdinand, while Manchester City defender Joleon Lescott has also been called into the squad.