The Argentina international’s season has been interrupted by a series of injuries, the most recent of which came during his side’s 5-1 hammering of Tottenham last month when he tweaked his hamstring shortly after opening the scoring.
Pellegrini had been hopeful that Aguero would be fit enough to make the substitutes’ bench for the visit of Tata Martino’s side, having stepped up his rehabilitation with a return to first-team training last week.
However, the City manager confirmed Monday: "Aguero is not on the squad list. We'll see if he can be fit for Saturday [against Stoke], but maybe it's difficult."
Aguero has scored 26 goals in 25 appearances this season, including six in the Champions League, and his head-to-head clash with international teammate Lionel Messi was due to be one of the most intriguing aspects of the match.
Pellegrini, however, is hopeful that midfield enforcer Fernandinho will be ready to make a return from injury after missing the last three games with a muscle strain.
“[Fernandinho] has a chance, he’s in the squad list for Tuesday, we’ll see tomorrow — he worked without any problem,” he added.