The Chelsea winger was forced off in the 39th minute after taking a kick to the ankle. He later left the stadium on crutches, raising concerns over the severity of the injury.
England Under-21 manager Lee Carsley confirmed that Gittens had been withdrawn as a precaution.
"Jamie got a kick on his ankle. We never take any risks," Carsley said.
Gittens has since returned to Chelsea's training ground at Cobham, where the club's medical team will assess the injury and determine the extent of the damage.
There is currently no confirmed diagnosis or recovery timeline, with Chelsea expected to provide more information after further tests.
West Ham winger Divine Mukasa has been called into the England Under-21 squad as Gittens' replacement.
The injury comes during a difficult spell for Gittens since his move to Chelsea from Borussia Dortmund for a reported 52 million pounds. The winger has found regular first-team opportunities harder to secure under manager Xabi Alonso.
Chelsea's next Premier League fixture is against Bournemouth at Stamford Bridge on Saturday, 10 October, although Gittens' availability for that match will depend on the results of his medical assessment.
Anthony Gordon believes his move from Newcastle to Barcelona has changed perceptions of him, with the England international feeling his technical and tactical qualities are finally receiving greater recognition.
Martin Odegaard has missed Norway's training session on Tuesday after picking up an ankle problem during the 2-1 Nations League defeat by Portugal.
Martin Odegaard was left angry after being caught by a late challenge from Portugal midfielder Bernardo Silva during Norway's 2-1 Nations League defeat in Oslo.
Thomas Tuchel has ruled out rotating his England team despite a demanding run of UEFA Nations League fixtures, insisting his players must be ready to perform whenever they are selected.
