Sheffield Wednesday chief Garry Monk rues controversial goal - as Manchester City counterpart Pep Guardiola hails 'incredible' Barry Bannan
Aguero continued his outstanding record in the Cup by sending City through to the quarter-finals with the only goal of the game at Hillsborough.
City were full value for victory on a night when the Owls were deservedly afforded plaudits at least for showing renewed character, organisation and fortitude on an occasion when their efforts were appreciated by home supporters at the final whistle - a far cry from the jeers and chants of 'You're not fit to wear the shirt' in Saturday's poor loss to Derby County in the Championship.
But Monk admitted that City's winner - on an evening when they spurned a number of chances and were dominant - still left a bitter taste in his mouth.
Monk, who confirmed that defender Julian Borner and Kieran Lee came off with injuries, said: "Overall, it was disappointing to lose the game, especially on a goal that should have been offside.
"I would have rather have lost it to a goal that was legitimate, but that is not taking away anything from Man City, who are fantastic.
"It was a difficult game, but we stuck at what we needed to do. I was disappointed with the result, but happy with the level of commitment and performance we took against a very good side.
"We understood how hard this game was going to be and what Manchester City force you into and we had planned for that.
"You could see what we were trying to do. You can go two ways, you can either go all out and trying to press them, but they have the quality to beat you and leave a lot of space for them.
"They also have the quality to force you to defend and still beat you in that way. But I thought in terms of the game plan we had and the competitiveness and organisation of what we needed to do and the concentration that the players did exactly what I asked them to do.
"They delivered it at a very good level.
"It was a bit unfortunate that we were forced into some early substitutions due to some injuries, which did not help towards the latter stages. The plan was to get to the latter stages intact and still in the game and freshen it up and make a few tweaks and have a good go.
"We tried to do that, but there was a few tired legs."
Questioned on his take on Wednesday's performance, City manager Pep Guardiola said: "I am not a guy to judge them. But we knew the physicality and Bannan is an incredible player with quality to make the passes for the fast players up front.
"I think they looked for players who are faster, which is why they did not play with (Atdhe) Nuhiu. But we controlled it and did not concede many set-pieces and in the second balls, we were good and deserved to win."