Goals from Sergio Aguero and Javi Garcia put the champions 2-0 up at half-time, but a much-improved performance after the break saw them pull a goal back through top scorer Demba Ba and go on to dominate possession and chances before a Yaya Toure goal 12 minutes from time saw their hopes of a point fade.
Perch feels Newcastle showed vast improvement from recent performances though, with the club currently on a run of six losses from their last seven games.
"I think most of us were gutted," Perch told The Chronicle.
BA OPEN TO ARSENAL SWITCH
Demba Ba is 4/1 with William Hill to open the scoring against QPR this weekend
"We kicked on and it looked as though we were going to score again, but they got the sucker punch of the third goal, which knocked the wind out of us and killed the game.
"We’ve got to be pleased though, especially with the second half. That’s when we played our best. I think we shot ourselves in the foot a little bit in the first half by not playing as well as we can do for a spell of 15, 20 minutes.
"We were up against the champions, and more than matched them for long periods of the game. They were just a bit more ruthless than us."