Guardiola named Gabriel Jesus as a lone striker at the Vitality Stadium, meaning Aguero had to make do with a place among the substitutes.
“Come on City!!!” Aguero tweeted shortly before the teams were announced. “Vamos! I am ready for the game!!”
Left-back Benjamin Mendy made his first appearance for City following his £52 million ($67 million, 56.2 million euros) move from Monaco, having previously been sidelined by a thigh problem.
Mendy’s former Monaco team-mate Bernardo Silva was awarded his first City start as Guardiola abandoned a back three and reverted to a 4-1-4-1 system.
City won 2-0 at Brighton and Hove Albion in their opening game, before drawing 1-1 at home to Everton last Monday.
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