"Cahill was assessed by England medical staff on Monday and will not be able to take part in the match but will be reassessed later in the week with a view to the qualifier against Montenegro on Tuesday," the FA said on its website (www.thefa.com).
Newcastle United's Steven Taylor has been drafted in as cover and could be in line for a surprise debut after a host of pull-outs from Hodgson's original squad.
Manchester United's Rio Ferdinand withdrew on Monday having been in line for his first international appearance since 2011.
Tottenham Hotspur captain Michael Dawson also withdrew from the squad, meaning Hodgson's options in central defence are looking threadbare with a lack of experience that, while unlikely to be a problem against San Marino, will be a concern against Group H pace-setters Montenegro.
Joleon Lescott, who struggles to hold down a starting berth with Manchester City, was Dawson's replacement and, with 24 caps, is the most experienced central defender available to Hodgson.
Manchester United's Chris Smalling (four caps) and Tottenham Hotspur's Steven Caulker (one cap) are the other options. (Reporting by Martyn Herman; Editing by Clare Fallon)