"I think it's not going to happen", Guardiola said "My desire, I think it's not going to happen".
"Last season I was asked many time and I said Sergio is going to stay until he decides his time here is over".
"I said not too much [will change] but it depends on the players", he said. "But in football you never know".
Aguero, who has scored 199 goals for City, is now sidelined with a knee injury.
"The chairman and myself want him to stay a long time".
The 23-year-old has reportedly chose to delay talks over a new contract with City until after the World Cup.
"That is now not in my head because, like I said to your colleague, I go on holiday in two days".
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"We made a good, high investment last year because it was an old team - 10, 11 players more than 31 years old". "That is no doubt about that, we have done that all season". Now we will make some changes with Yaya leaving. So, one or maybe two. "It is hard to find anyone better than Bernardo Silva".
The Portuguese has featured in all but four of City's 56 games this season but only 27 of them have been starts.
"Maybe I will be concerned by that and maybe they will be in the line-up, maybe they will play".
Midfielders Phil Foden and Brahim Diaz are now one short with four apiece and could miss out.
The Citizens' 3-1 win over Brighton & Hove Albion in midweek brought up a number of records, including most goals scored in a single Premier League campaign and most points accrued with 97.
The Premier League only ensures players who have played in a minimum of five games receive one, but clubs are permitted to hand out extras to whoever they see fit from an allocation of 40.
"They are champions, from the first day in the locker room".