The Argentine has been a mainstay for City over the past decade, but is now nearing the end of his time at the club.
He may not renew his contract at the end of the season.
Guardiola knows he has to plan for a future without Aguero sooner than later.
"We need him and we miss him because his numbers speak for themselves. He is the best striker in our history," Guardiola told reporters.
"He can create and win games for himself. We could have complained (about being without him), but we did the opposite.
"We want him back, but we have to move forward, find alternatives, use the quality we have and move forward."