In an eventful derby clash in which City threatened to come back after going 3-0, United held on for a 3-2 win.
It was a game full of talking points, involving Vincent Kompany and Paul Scholes amongst many others.
Here are six things we learned about Manchester United in the FA Cup third round match at the Etihad Stadium.
Despite being up 1-0 at the time, it's clear Manchester United was helped by Vincent Kompany getting sent off.
The red card handed out to the centre-back was clearly wrong, despite the letter of the law technically labelling a sending off offence as one which is wreckless and/or uses excessive force.
The decision took the sting out of Manchester City and was the deciding factor in the match.
Fitness-wise Paul Scholes seemed fine against Manchester City. But in terms of overall match practice, it's clear the Manchester United legend is a bit rusty.
It was his error which led to the Sergio Aguero goal that gave City momentum, while none of his Hollywood-style passes were on display.
Perhaps it would have been better to introduce Scholes in a less challenging and less highly-charged game.
Anders Lindegaard showed off his quality yet again today against Manchester City, most notably in the first half with a sensational diving save to deny Sergio Aguero.
It follows six consecutive clean sheets the Dane kept prior to this match, and the Newcastle United one in the Premier League.
Lindegaard was unable to prevent both goals he conceded on Sunday despite his best efforts, and should be considered United's No.1 player ahead of David De Gea.
Despite rumours of wanting to leave Manchester United and a bust-up with Sir Alex Ferguson, Wayne Rooney let his actions on the pitch do the talking against Manchester City.
Overall, he was United's best player at Eastlands, not least of all due to his two well-taken goals which included a brilliant header to open the scoring.
He deservedly won the Man of the Match award, and could now kick on in the Premier League to challenge Robin Van Persie and Sergio Aguero for the Golden Boot.
Not only is Antonio Valencia better as a winger than a full-back, he's also Manchester United's best option on the flanks.
While Nani is a better finisher, Valencia is by far the better player at putting in a decent cross and retaining possession of the ball—the two most important things United require from their wingers.
If United are to push on from this win and mount a serious challenge for the Premier League title, they'll need to get their proper full-backs fit soon and allow Valencia to play further up the field—i.e. in a position where he'll really be vital for the Red Devils.
As Sir Alex Ferguson said in his post-match interview, this match gives Manchester United no extra momentum in the title race.
They will probably gain some sort of psychological boost for knocking out their bitter rivals and current FA Cup holders.
However, by allowing City to regain some momentum in the match and put in a spirited performance which will give them encouragement, United's win is empty.
United will need to do the same over City in the Premier League before they can really have the proper momentum to win the title.