The trio were notable absentees from the 19-man list, which made the trip to France for Tuesday night’s crucial Group F clash.
Speaking in his pre-match press conference, Guardiola explained they did not travel due to fitness issues.
“Bernardo Silva is in the last step before being fit,” he told press.
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“Gabriel Jesus had had a muscular problem in training but isn’t ready.
“Ilkay Gundogan had a problem in his feet.
“I prefer to have all the squad to choose but it is what it is. We have to adapt with the guys that are here and will try to do a good job and the others who aren’t here will do their best to recover.”
Youngster Phil Foden was one of the names included in the squad list.
Asked whether he feels the midfielder is ready to feature in France, Guardiola replied: “Definitely.
“When he appeared in the last pre-season, I was so impressed.
“He is now stronger and able to play with us – without a doubt.
“He plays so aggressively with the ball and without, he is so intense. Every time he plays, he is so good.
“That’s why he is ready. He is part of the squad.”