He maintains City's relative lack of pedigree at the elite level - their solitary Champions League semi-final appearance ended in a limp 1-0 aggregate loss to Real Madrid in 2016 - means the situation at the Etihad Stadium is different.
Aguero, though, has fully reestablished himself as Guardiola's first choice in Jesus's prolonged absence by doubling his tally for the season in the last two months to move onto 30 goals for the campaign. And that might be a problem.
In his post-match press conference, Guardiola fumed about how his team "forgot to play" in their defeat, and said that what they produced wasn't football.
While the game may have been a dead rubber, Guardiola would have wanted to keep his unbeaten run at home this season intact.
It is his all-round game, too.
Having booked a place in the Champions League last eight against Basel in midweek, Guardiola takes his side to Stoke on Monday evening and is adamant performance levels can not drop if we are to fulfil ambitions this season.
Pep Guardiola had the opportunity to rotate for this game after the comfortable manner in which City won the first leg, thrashing their Swiss opponents 4-0. City's passing was often sloppy and Basel broke regularly through a home midfield featuring the 34-year-old Yaya Toure - the captain for the evening - and a player half his age, English prodigy Phil Foden.
Jesus might have to bide his time now, which would be frustrating for the Brazilian after his recent time out of the team with knee ligament damage and the fact that he will be looking to impress Brazil coach Tite with only three months to go before the World Cup in Russian Federation.
"You will find in all the clubs in the world", Guardiola said, "that when you make six changes, the team is not the same".
"It's good for the rhythm of the future".
That team dominated the last 10 years.
English referees chief Mike Riley was at City's training ground for discussions with director of football Txiki Begiristain on Tuesday, following Guardiola's complaints that players should be more effectively protected from unsafe challenges. We tried, we spoke about that and I think what we showed in the first half we showed we wanted to win the game. Gonzalo Higuain and Paulo Dybala scored goals in the space of three minutes as Juventus came from behind following Son Heung-min's opener.
With the Swiss side making most of their attacks down the left against Danilo, the Brazilian was beaten for pace constantly and was lucky to not be booked for a foul in the first half which would have seen him suspended for the quarter-final first leg.
Guardiola suggested at the end of last month that the club would offer the teenager a new long-term contract when he turns 18 in May.
However, the coach hopes a three-week break following Monday's league trip to Stoke will leave his side refreshed for the last eight.
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