The Man City full-back has been a regular selection for the Three Lions in recent campaigns, but has not been picked for the clashes with Bulgaria and Kosovo.
England boss Gareth Southgate has instead opted to choose Trent Alexander-Arnold, Kieran Trippier and given a first call-up to Aaron Wan-Bissaka.
Walker has started the season in good form for his club side, and Guardiola has backed him to regain his place in the international side.
“I was a little bit surprised at first,” Guardiola said.
“I’m not involved. We’ll respect the decision. Kyle is coming back stronger. I understand him and support Gareth.
“I’m pretty sure the players want to go to the national team. It’s happened, so we adapt.
“We have time with our family now with the international break. Come back and play as best as possible to come back to the national team.”
Walker has 48 England caps to his name compared with the relatively inexperienced Alexander-Arnold on six – while Trippier (17 caps) returns to the squad after missing out on the UEFA Nations League.
But after dropping Walker from his squad, Southgate revealed his reasons behind the decision.
Southgate said: “We have got to qualify so we’re always mindful of the need to keep winning matches.
“But, also, we’ve got to give some opportunity to develop other players.
“Without getting Trent’s head too big, too quickly, he’s one of those we look to integrate and give more opportunity to.
“If we don’t make a pathway, then when are you ever going to put them in?
“With Aaron, we’ve got a completely different kind of player and we’ve got Trips as a bit of cover. So there’s no point bringing Kyle in if the intention is not to start him in games.
“He’s a senior player and he’ll value the rest and recovery. But we could be in a different space in four weeks’ time.
“It’s a unique position to have four that are of a very high level, but two young ones as well.”