With the FA Cup final against Manchester United just six days away and the Champions League final a week later, the boss revealed that many of the seven changes he made for Brentford were enforced.
But he added he was hopeful most, if not all, of his squad will be available for next weekend’s Wembley derby.
“We have four or five players with niggles, not big injuries, but they are injuries,” said Guardiola.
“The guys who didn’t play didn’t here were really, really exhausted the day before and mentally, they were completely drained.
“The guys who are in Manchester - Ruben didn't train for 10 days, Jack Grealish, as well.
“After the game against Brighton, Kevin felt the same feelings that he had before, weeks ago when he could not play a few games. It is what it is.
“It's not a big issue, I think they will be ready. They have to be ready for the training sessions and I am going to see them in three days and that's why today was so important to see these players and how they are.
“Phil is in incredible form, Riyad as well, Cole was so active in many things.
“To play the finals we have to play the guys who feel better. Not because they played a lot of minutes.
“That’s why it was good to play with these guys and rest the other ones and hopefully the other ones can recover.
“The guys who played today deserved to and it’s important for me to see how they feel.
“And Nathan (returned) after being injured. Aymer (Laporte) came back again and played 90 minutes.
“Unfortunately for Kyle I could not give him time to rest because we didn’t have many substitutions.
“But they needed to rest now, to arrive with the right energy and that is going to happen against Untied and after in the next game in the Champions League.
“Wednesday they will train and recover tomorrow. Hopefully (they will be OK), but right now, I don’t know.”
Guardiola added that he had no complaints about the 1-0 defeat to Brentford who he called an “exceptional” team.
“Congratulations to Brentford for the victory,” he said.
“It was a tight game. They pushed more and it was difficult to face them.
“How quick they play, how aggressive and fast in all departments. But I don’t have any complaints, how good we behaved, and all the players were there.
“I said to the players after the game, today we finished the Premier League, that you deservedly won.
“Enjoy two days with your families, don’t see each other and on Wednesday we’ll prepare the first final.”