Referee Mike Riley was the villain of the piece as he gave the visitors what looked a debatable penalty on 77 minutes.
Substitute Daniel Sturridge went down in the box with Nyron Nosworthy in close attention and Riley had no hesitation in pointing to the spot. The official also booked Nosworthy, but replays showed there was little if any contact.
Sturridge did leave the field immediately afterwards unable to continue and it was his replacement, Darius Vassell, who would deal the killer blow.
Before that though, Brazilian Elano stepped up to send Sunderland keeper Craig Gordon the wrong way and give City the lead from the spot.
The Wearsiders however, weren't about to go down without a fight and looked like they might have rescued a point minutes later.
Andy Reid reached the byline down the left flank, before whipping in a great cross for Dean Whitehead to hit a superb volley into the roof of the net from inside the 18-yard box.
The strikes brought the game to life, for in truth the whole first half and the early stages of the second had been a fairly turgid affair.
Neither side really managed to get to grips with the conditions as heavy rainfall made the pitch slick and greasy.
However, even without the downpour this was a fairly dour viewing for the crowd of 46,797.
The only real attack in the opening 45 minutes went the way of the home side, when Kenwyne Jones was denied from a brave save by Joe Hart in the City goal.
Jones looked to lift the ball into the net, but the Blues' stopper saved bravely at his feet.
After the break things continued in much the same vein, that was until the intervention of Mr Riley.
The man in the middle was over-officious all afternoon and did little to endear himself to the home fans.
And as if pointing to the spot wasn't bad enough he had a hand in City's winner.
Sunderland lost possession in the middle of the park in the 83rd minute and substitute Grant Leadbitter slid to win it back.
However, his route to the ball was blocked by the body of Riley, who was standing in his way. City broke and the ball fell to Vassell. Then to add insult to injury, he scuffed his shot and the ball trickled into the net.
It was one of those days for the home side, but really they should have punished City when they had them on the back foot.
The fact that they didn't and Mr Riley's spot of bother means Roy Keane will have to wait to ensure Premier League safety.