It looked as though the two Premier League sides had cancelled each other until the Argentine full-back intervened five minutes from time.
Below, Sports Mole has looked back over the encounter to determine if the home side deserved to come out of the tie with a replay.
On target 4
On target 8
Was the result fair?
On paper, a 1-0 victory always gives the impression that a match was closely contested - not this one! Visiting City were the dominant force from the first whistle and probably should have been a goal or two up at the break. As it was, a late goal from Zabaleta got them through and they thoroughly deserve to be in the next round of the competition.
Tony Pulis's side have earned themselves a reputation over the last few years as a side that gets stuck into their opposition and uses their physical presence to their advantage. None of that was on show today though. Defensively they were poor and gave players like David Silva far too much space in dangerous areas of the pitch. Meanwhile, up the other end they were pretty toothless and never gave the impression that they were going to score.
Man City's performance
The main criticism of City, as harsh as it may be, was that they only won the match 1-0. During the first half they controlled the match and while after the restart their football didn't flow as freely, they eventually got the goal that their performance warranted. On that form, they are arguably favourites to go and win the trophy for a second time in three years.
Sports Mole's man of the match
Pablo Zabaleta: When Vincent Kompany limped off early in the match, Zabaleta took on the captaincy duties and put in a performance that the armband demands. He won numerous tackles and even got the better of the likes of Peter Crouch in the air! The crowning moment came when he started and finished the move that resulted in City scoring the winning goal.
Chances were few and far between for Stoke, so when they created one, they couldn't afford to waste them. That is exactly what Cameron Jerome did as the match ticked into stoppage time when he fired well over the crossbar from 10 yards out.
Howard Webb is widely regarded as England's best referee and while he proved that for large parts of this tie, he failed to send off Glenn Whelan for what was a shocking two-footed tackle on Javi Garcia. It's one that the Football Association may punish come Monday morning.
Stoke: Premier League clubs are in action during the week, with Stoke City playing host to Wigan Athletic on Tuesday evening.
Man City: On the same night the champions travel to Loftus Road for a clash with struggling Queens Park Rangers.