Kevin De Bruyne will be out up to six weeks after suffering ligament damage in his left knee.
De Bruyne was making only his second start since a three-month absence following ligament damage to his right knee.
In January 2016, De Bruyne also seriously injured his right knee and ankle ligaments.
Pep Guardiola said: “We are sad for him. Nobody likes to be injured. Unfortunately he is injured but fortunately it is not surgery.”