City were missing the spine of their team in Vincent Kompany, Yaya Toure and Sergio Aguero as Mark Hughes' side, buoyed by the brilliance of Xherdan Shaqiri and a Marko Arnautovic brace, consigned Pellegrini's men to defeat.
Having already qualified for the Champions League knock-out stages - and progressed to the last four of the Capital One Cup in midweek - City's schedule is hectic and Pellegrini believes his inability to shuffle his pack due to injuries is leaving his side jaded.
"We are playing in other competitions with the same 13 or 14 players," he noted
"For me, seeing the game, without doubt they didn't recover from the last two games
"In this game we are playing with the same players in the last three games - maybe it's the reason why we didn't play with the energy that we need to win."
The Chilean's options will not increase for Tuesday's trip to Borussia Monchengladbach either as neither Toure or Aguero will return while Fernando was forced off with a hamstring injury in this contest.
Pellegrini cited too many games, a lack of preparation time and the international breaks as possible reasons for their flat showing against Hughes' side, but denied they are lacking figureheads in the absence of Kompany, Toure and Aguero.
"I don't think there's a lack of leaders," he added.
"So far this season we are the only team that is involved in all of the competitions that have qualified for (the Capital One Cup) semi-final, that we are top of the table in the Premier League and we qualify in the Champions League
We play very bad because we are playing with the same 12, 13 players, and nothing much more happens."
City were able to name David Silva, Raheem Sterling and Kevin De Bruyne in their starting line-up, for the first time since they scored six against Newcastle in early October.
However, it was the creative flair of Shaqiri, who created both of Arnautovic's goals, who sparkled on a blustery afternoon.
"On the day we were exceptional," said ex-City boss Hughes.
"We had a game plan as we always do, We knew what we needed to do well
You can talk about tactics but the guys need to go out there and execute them and that is what we did.
"We had a number of chances
In terms of clear-cut chances we were way ahead of City on the day and we could have easily made it embarrassing if I'm honest, but I'm happy with two goals."
It was a memorable day for the enigmatic Arnautovic, who would have claimed a four-goal haul in the first period had his header hit the other side of the net and his one-on-one hat-trick chance not struck the post.
The Austrian has not always reached such heights during his time at Stoke, while he spent the post-match celebrations arguing with City's players rather than basking in the glory, and Hughes challenged him to find some consistency.
"He is a big personality," Hughes admitted.
"He is a great guy, someone who came to the club having been undervalued at other clubs
What he has had this year is a really good start to his season compared to other seasons when he started slowly
The test for him is he needs to keep going from now until the end of the season."
Source : PA
Source: PA