Central defenders Ruben Dias and John Stones were ruled out through injury while he delayed a decision about playing Nathan Ake and Manuel Akanji until as late as possible.
He also revealed that Kyle Walker returned to the starting line-up after one training session following three weeks out injured.
Ake was replaced midway through the second half but Guardiola is hopeful that he can have the bulk of his squad back together soon.
“The players have made an incredible effort because there are players that are not in the best way and they made an incredible effort to be here,” he said.
“So Manu, Nathan were not in really good conditions. Until the last moment I didn’t know if Nathan could play and he said ‘I want to try, I want to try’.
“That’s why after 2-0, we decide to pull him because we need him for next Tuesday in Lisbon. That’s why. It is what it is.
“Sometimes there are seasons where this happens more than the other ones. We have to handle it, people come back and sooner or later the team will be back.”
On Walker, he said: “Kyle, 18 or 19 days and only one training session with us and today he was there.”
Watch the full press conference in the video above…
