Aguero has been linked with moves to Chelsea and Tottenham following news that his 10-year stay at the Etihad Stadium will end in the summer.
Barcelona, Juventus and Paris Saint-Germain have also registered their interest in the striker but Guardiola said he is happy for the 32-year-old to stay in England, even if it means his arrival strengthens a title rival.
"The best for him, we wish, all of us," Guardiola said at a news conference on Friday. "Find the best for Sergio for the last years in his career, for sure. We'll be delighted with the decision he takes, the best for him and his family and his career.
"My preference is his preference. His preference is my preference. The best for him is the best for us."
Aguero has averaged better than a goal every two games since moving to City from Atletico Madrid in 2011 but has struggled for form and fitness this season, scoring just three times in 15 appearances.
Guardiola's side are still chasing four trophies in the final weeks of the season and insists he still needs him.
"Everyone must be ready and hopefully Sergio can be ready quick," Guardiola added.
"Sergio is a lovely person with specific qualities and skills. I understand him, I know him, and I understand he needs time to get in the best condition.
"I said last week. After we announced [his departure] the way he trained, and in the Leicester game, which was so difficult because they defend so deep and so tight, for the strikers it is not easy, he moved well and helped us. He felt something in his leg [and] he was substituted. He is doing better."