He said: "That was not the same team as on Saturday, without any doubt. Maybe we couldn't recover so soon after three days to have the same pace that we had against Chelsea.
"We knew also before the game that it was going to be a very tough game because Newcastle are playing not to be relegated next season. They had just won their last game, so it was a difficult game as we expected."
Pellegrini was at least able to revel in Aguero's achievement with only Newcastle old boy Alan Shearer having reached a Premier League century in fewer than his 147 appearances.
He said: "I am happy for him because it's not easy to score 100 goals in the amount of games that Sergio did it.
"He's second in the history of the Premier League, so I am happy for him and I hope he will continue the same way until the end of the season."