Aguero, 32, has stepped up his recovery work in the gym and although he has yet to return to the pitch, the City boss says he will have a full squad for the second leg at the Etihad Stadium, minus the suspended Benjamin Mendy.
"I think against Madrid everyone will be fit," Guardiola said ahead of Sunday’s final Premier League game against Norwich.
"Mendy is suspended but the other ones will be fit and I think in two weeks, barring a disaster in the training session that hopefully won't happen, everyone will be fit and we're going to count on the senior guys for this game."
Aguero was left on the bench for the 2-1 first-leg victory at the Santiago Bernabeu but having him available will be major boost, particularly with the quarter-finals to follow quickly after.
With second place already secure, Guardiola is focusing the next two weeks on their European challenge and wants to see an improvement on recent performances, particularly the disappointing FA Cup loss to Arsenal.
"We want to prepare the right way for Real Madrid," he said. "The game against Norwich and how they train this week will be what I base Madrid on. Every game will be an exam for me to see who is ready to play the game.
"Against Watford [we were] a little bit better. But still we need to improve."
The 29-year-old is currently on 19 - one behind record-holder Thierry Henry - ahead of the visit of rock-bottom Norwich City.
Despite being beaten to the Football Writers’ Association Footballer of the Year by Liverpool captain Jordan Henderson, Guardiola says his contributions are clear to see.
"I think [Kevin] speaks for himself what he gives to our team," he said. "It’s not necessary to say how fantastic Kevin is. At the same time, congratulations to the captain at Liverpool. He’s a really good player.
"[Kevin] enjoys making assists, he’d love not to score millions of goals, he makes assists, but he’s taken penalties and free-kicks and taken responsibility to score goals which is most difficult thing.
"Not just this season, the numbers, the way he’s played is incredible. In the 100-point season, I’ll never forget how he played in this incredible milestone."