Aaron McLean scored the winner for Hull as the Tigers came from behind to move up to sixth in the Championship table.
Chris Wood put Birmingham ahead by driving the ball into the bottom corner from just inside the area.
Just after the break Robert Koren volleyed past Boaz Myhill after Cameron Stewart's pass deflected into his path.
McLean latched onto Koren's pass and slotted home for the winner, but goalkeeper Myhill should have saved the low near-post shot.
The win will strengthen Nick Barmby's claim to take the Hull manager's job on a full-time basis. His side were spurred on by the performance of former Manchester United winger Stewart, who tormented Birmingham throughout.
Birmingham's goal came against the run of play after Hull had spurned a number of chances. Blues also survived a penalty appeal when Pablo Obanez brought down Matty Fryatt in the box.
After Koren's goal, Birmingham struggled to respond and could have gone behind when Jack Hobbs nodded over the bar from Koren's right-wing corner.
Despite Hull's domination, the visitors might have snatched a point but Peter Gulacsi thwarted Chris Burke's close-range header.
Hull caretaker manager Nick Barmby: "The ambition [for Hull] is to be up there. The team we've got, they should be believing they can challenge and there's no reason they can't.
"If they show that application week in, week out they've got a great chance. But it's a difficult league and you just need to be more consistent.
"We've asked them for consistency at home and they've managed to win the last two, which is pleasing. I'm really thrilled, it was an important win for us tonight."
Birmingham boss Chris Hughton: "We're on the back of four tough away games now, having gone to Blackpool, Braga, Cardiff and Hull. That's a tough period in any season.
"Over 90 minutes we certainly had enough chances not to lose the game. We're victims of not being clinical enough with the good chances we had and not defending well enough over 90 minutes.
"It's frustrating because, if you look at the chances we've created, we shouldn't have lost the game. But one thing about a difficult time is you've always got the opportunity to put things right and go on another good run."