The pair helped the Ivory Coast to continental silverware during January and February, with City struggling in Toure's absence.
Bony - who arrived from Swansea City in January - has yet to get off the mark for his new club and Pellegrini feels their AFCON involvement has hampered their recent form.
"It was important for [Bony] to start the game from the beginning," Pellegrini said of the striker's full debut in Wednesday's 2-0 win over Leicester City.
"He only played a couple of minutes in the last few games and he only just arrived from the African Cup of Nations, where they played a lot of games.
"I think Yaya [Toure] is also feeling the pace of the games.
"It would have been better for [Bony] to score, but it was more important to start a game, it was also important for him to have some chances and I think he worked very well."
