"He (Aguero) is coming back from injury. He hasn't played for a few weeks," Bony told British media.
"I'm disappointed that I didn't start but I'm not the coach. The coach does what he thinks is best for the team."
The former Swansea City forward had scored three goals in four games leading to the clash at the Emirates Stadium, although Aguero is the club's topscorer this season with nine goals, two more than Bony in five fewer matches.
Pellegrini backed his decision to start Aguero.
"He worked with the squad the whole week. He needs minutes," the former Real Madrid manager said.
"Normally when he comes back from an injury he needs minutes. I think that these minutes will be very important for him."
City, who are third in the table, are four points behind Arsenal and six points behind shock leaders Leicester City.
Pellegrini's charges host relegation-threatened Sunderland in the league on Saturday, before travelling to meet Leicester on Tuesday.
Pellegrini hinted that skipper Vincent Kompany could be fit to face the Black Cats.
"With Vincent returning to the team, with David (Silva) and Sergio playing normally every week I suppose that we are going to continue being an important team for the fight of the title," Pellegrini said.
(Reporting by Chris Peters in Bengaluru; editing by Sudipto Ganguly)
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