The Blues boss revealed on Saturday that the Argentine striker had been playing with a foot injury since the triumph over Newcastle, adding that he was substituted against Brighton as a precaution.
With Gabriel Jesus available for selection, Guardiola told press he will make a decision on matchday on who will start upfront.
“Tomorrow is such a big game and he (Sergio Aguero) is here because the doctors said he is able,” the Catalan manager stated.
“Tomorrow, we will decide whether to play him or Gabriel Jesus.”
Guardiola also provided updates on Kevin De Bruyne, who returned to training on Monday, Fabian Delph and Benjamin Mendy.
GALLERY: Open training | De Bruyne is back!
“KDB isn’t here because he still is not able to play,” he continued. “We have missed his quality but he’s back.
“Today was the first training session with the team so we will see when he’s ready.
“Delph, no (he is not fit and will not play against Liverpool on Sunday). Mendy, maybe. We have enough days until the game so hopefully.
“The problem is, they still haven’t trained with us. When we return, they can train with us.”
With City having lost the Group F opener at home to Lyon, Guardiola asserted the Blues must treat each remaining European game as a final.
“We have five finals ahead in the group stages,” he said. “In the Champions League, we don’t have time to lose a lot of games. Tomorrow is the first final.
“We need to review the game against Lyon. Maybe in the first half, we were not like we normally are.
“It’s the Champions League so all of the teams are good. I give credit to the opponents.
“Like Vincent Kompany said perfectly (earlier in the press conference), it’s a top quality competition and it’s so complicated.
“It is a tough competition for all of us and we try to be stable. I think we are making steps forward because in the last few seasons, we have qualified quite comfortably.”
Guardiola also added he is looking forward to meeting Hoffenheim coach Julian Nagelsmann and asserts his side must not underestimate the German outfit, who held Shakhtar Donetsk to a draw in Matchday One.
“I sent him a text,” he explained. “Tomorrow will be the first time we will have met each other. We talk about young players and talent.
“Of course, I’m really impressed. He is so young and they keep getting better and better.
“He will have a lot of success in his career. He is already managing a good team in a top competition.
“I’m looking forward to facing him and hopefully, this season won’t be the last time we play each other.
“I’ve already played (Hoffenheim) two or three times. Villarreal is a small town but they go far in the competition. It doesn’t matter how big the town is – it’s about how you play on the pitch.”