Hart was expected to regain his place in the side after being rested for the 7-0 mauling of Sheffield Wednesday in midweek, but Pellegrini installed Willy Caballero between the sticks for the second game running.
There are question marks as to when Hart will return to the side, after being dropped for a period of games last season by Pellegrini following a series of high-profile mistakes.
"I think for Willy it was good to play not just one game but to play two in a row," the City manager told Sky Sports after the game.
"Joe played eight games in 32 days, a lot of games for a goalkeeper. I have a squad of 22, 23 players and I make rotations because I think it is better for the team.
"In this case I think it was good for Willy."
Pellegrini will have to decide who to play in goal on Tuesday, when they host Roma in the Champions League.