Ole Gunnar Solskjaer called for the spirit of Paris St Germain and the "perfect performance" as United attempted to bounce back from their chastening 3-1 semi-final first-leg loss on home turf.
But their feeble first-half display at Old Trafford three weeks ago ultimately proved their undoing, with Nemanja Matic securing a 1-0 win on the night only for City to progress 3-2 on aggregate.
"We will definitely take the positives from the game," United skipper Maguire said. "The dressing room, at the moment, is disappointed and a bit flat.
"It's strange because we have won the game and we've done well on the night, but the first 45 minutes at Old Trafford has cost us the tie.
"We were arguably the better side in the second half at Old Trafford and then we have come to the Etihad.
"We knew it was an uphill task, we gave ourselves every chance in the second half but it just wasn't to be."
United ended City's 19-match unbeaten run in domestic cup competitions as they won consecutive away matches at their rivals for the first time since triumphing in four-straight matches between 1993 and 2000.
Last month's 2-1 win and the victory on Wednesday show what Solskjaer's side can produce, but they were just unable to ratchet up the pressure on a night when goalscorer Matic was sent off in the closing stages.
"It is tough to create chances here," Maguire said.
"They are a good side and they have proved it over the last five years. At half-time we were in the perfect position.
"We wanted to stay in the game until the last 20 minutes, when we knew we could create momentum and pressure, like we did at Anfield.
"It's hard enough to get the ball off them when it is 11 v 11.
"We obviously lose Nemanja, who was excellent on the night, so there is no blame on him, but it was difficult when we went down to 10."
Matic will miss Saturday's Premier League clash with Wolves through suspension as a result of the sending off.
United have a much-needed two-week winter break to look forward to after that Old Trafford clash and skipper Maguire underlined the need for a win.
"Yeah, it is really important," the England defender told MUTV.
"One last big push before the lads can put their feet up and have a little rest, which I feel like we do deserve and we need.
"I think you saw in the second half that we looked a bit tired in our pressing.
"It is one last big push, we need a big result against Wolves, and we need to come out fighting and put on a performance."