Guardiola's side face Real in the second leg of their last 16 tie on August 7 as they look to protect a 2-1 lead from the first meeting in Spain.
Aguero has been sidelined since June 22 with a knee injury that required surgery in Barcelona.
Earlier this week, Guardiola had raised hopes that City's all-time record goalscorer could return for the clash at the Etihad Stadium.
But, speaking after City's 5-0 win over Norwich on the last day of the Premier League season, Guardiola was far less confident about the Argentine forward's availability to face the Spanish champions.
"I don't think it will be possible," Guardiola said.
Aguero has netted 23 times in all competitions this season.
Gabriel Jesus has deputised for Aguero and he scored against Norwich to make it four goals for the Brazil striker since the coronavirus hiatus.
City have never gone beyond the semi-finals of the Champions League, while Guardiola hasn't won the tournament since 2011 with Barcelona.