City took the lead in the first half through Sergio Aguero, but Jack Wilshere and Alexis Sanchez responded to put Arsenal ahead before a late goal from defender Martin Demichelis secured City a point.
Pellegrini feels that the result could have been different had referee Mark Clattenburg spotted some subtle fouls.
"I think it was a great game, two very good teams which try to play, both teams are very creative," Pellegrini told BT Sport after the game.
"Today both goals by Arsenal were very clear fouls, the first one, two or three continuous fouls and the second one [Danny] Welbeck on Vincent [Kompany].
"Wilshere had two hands in front of the linesman and it is a clear penalty, so in that case I must be very happy with the draw. We have more possession and more chances than Arsenal."
The draw sees City currently occupying third spot in the Premier League table.