The third meeting this campaign of the Manchester clubs looked like a case of familiarity breeding contempt in a scrappy and untidy first half littered with fouls and misplaced passes.
City went into the game on the back of four successive league games but this current form was lacking as they failed to create their recent fluency with skipper Steph Houghton unusually error prone at the back.
At least Utd had an excuse for the poor display, suffering a shock home defeat to Bristol City before recovering to outclass Tottenham 3-0 last time out.
Houghton had twice made mistakes which Utd should have punished so in the context of the game it was no surprise that the only goal of the half should be following an individual error by Utd, and former City defender Abbie McManus in the 30 minutes.
A woefully under hit back pass allowed Ellen White to pounce and easily chip keeper Mary Earps for the opener.
Georgia Stanway almost immediately doubled the lead but her effort was blocked by Earps.
It was fitting that White had scored as she had looked the most likely and was foiled by a fine save in the 15th minute in a half of few chances.
The nearest Utd came was a Jane Ross shot from distance which clipped the crossbar.
City began the second period full of purpose and should have increased their lead early on following a quick break which ended with Tessa Wullaert rounding the keeper but blasting over with White unmarked.
Utd also began to impress and suddenly we had a proper Cup tie on our hands but just as it seemed an equaliser was on the cards City struck. Lauren Hemp raced down the left wing, crossed and White was in the right place for number two.
Utd responded immediately but Ellie Roebuck saved well from Kirsty Hanson. But they were not to be denied and substitute Lauren James was allowed to turn and fire low into the net to give the home side hope.
They then thought had levelled through McManus but Roebuck stopped the ball on the line with the home crowd and players claiming it had crossed well over.
The joy was short-lived as City regained their two goal lead and eased the nerves with a precise finish from Jill Scott.
Bearing in mind the 'ball-over-the-line' incident Utd had every right to feel aggrieved with how fortune was treating them.
But with two minutes remaining they were handed a lifeline as Hemp scored own goal from a scrambled corner.
This saw five minutes of added time which City nervously negotiated before booking a place in the next round of the FA Cup.
Man Utd: 2 (James 69, Hemp og 88)
Man City: 3 (White 30, 56, Scott 76)
Venue: Leigh Sports Village Stadium