Aguero had previously been ruled out of the round-of-16 second leg at the Etihad Stadium on Aug. 7 with a knee injury.
- Stream FC Daily on ESPN+
- Insider Notebook: Lampard loses faith in Kepa; Jovic's Real nightmare
"I think against Madrid everyone will be fit apart from [Benjamin] Mendy, who is suspended," Guardiola told a news conference on Friday.
"In the training sessions everyone will be fit and we'll go for the senior guys for this game."
City have one final Premier League game against Norwich, plus two weeks of training, to prepare for Real Madrid and Guardiola said every player will be watched closely to find out whether they are ready to face Zinedine Zidane's newly crowned Spanish champions.
"The way they play against Norwich and the way they train, I will be paying attention for how they play against Madrid," Guardiola added.
City have nothing to play for against Norwich, who have already been relegated, but Guardiola has asked his players to focus on reaching 100 league goals for the season.
Four goals against Watford on Tuesday took them to 97 for the campaign so three on Sunday would take them to the century mark.
"It's nice to score goals," Guardiola said. "But it's not enough. It's a lot of goals but we are 18 points behind Liverpool. Every game there is a target, a desire to win the game and scoring 100 goals is one of the reasons why."