The Arsenal forward picked up a minor hip/groin injury in training on Thursday evening and has also been ruled out of the vital Group H game against Montenegro in Podgorcia.
Walcott was in the Serravalle Stadium on Friday evening to watch the game against San Marino and he will be assessed by Arsenal's medical staff when he returns to England.
Early reports suggested Walcott could be sidelined for up to 10 days, which could keep him out of the Gunners' Premier League match against Reading on Saturday week.
England boss Roy Hodgson delivered an update on Walcott following the 8-0 win over San Marino.
He told Sky Sports: "He's had to go home. He was at the game tonight watching but he will be going home tomorrow, there is no chance of him playing on Tuesday.
"It's a minor tear in an unusual muscle in the pelvic area. I don't know the exact details, but hopefully it won't keep him out for too long. It just makes certain he can't play on Tuesday."