Championship promotion-chasers Huddersfield grabbed a shock lead in the seventh minute at the Etihad Stadium through a Harry Bunn strike that Bravo should have done better with.
City then roared back in ruthless fashion as goals from Leroy Sane, Aguero - from the penalty spot - and Pablo Zabaleta had them 3-1 up by half-time.
Aguero subsequently added his second before substitute Kelechi Iheanacho wrapped things up late on.
Wagner, who watched the game from the stands in what was the first in a two-game touchline ban, felt his side did not show their true colours on the night, showing “too much respect” against a City side containing a number of top stars.
“Of course the start was positive because we went in front but we were not at our best, performance-wise,” said Wagner.
“We have shown too much respect, unfortunately, against a very strong Manchester City side.
“Congratulations to Pep. The result was fair. We made too many easy mistakes when we had the ball and when we defended we were not aggressive enough. When you play against Manchester City you have to be very aggressive.
“We were not good enough in our defensive third. We were not brave enough to play out and we allowed them to counter attack. We were second best; we were not at our best. We didn’t perform. Even if we had, it would have been difficult. They were very good today.”