The home team dominated the game for more than an hour, and then defended well when Hull took control in the last half-hour.
Hull didn't look a top three team as Hartlepool showed the sort of form that took them to last season's play-offs, and City boss Peter Taylor admitted he was disappointed.
Hartlepool started like a train, and they should have been ahead from the kick-off, when a great move ended with Richie Humphreys blasting wide as he ran onto a square pass from deep on the right.
But the home team went in front on seven minutes, Joel Porter blasting in from 15 yards after a neat pass from the left by Eifion Williams.
Hartlepool continued to dominate, and Humphreys forced a finger-tip save from Matt Duke with a close-range shot on 22 minutes.
Four minutes later, though, Hull should have been level when a free-kick wasn't cleared properly and Danny Allsopp found himself unmarked yards from goal, only for Jim Provett to twist in mid-air and save well.
Two minutes after the break, Hartlepool were close to a second when Adam Boyd hit the City bar from ten yards after a shot from Humphreys was blocked in a packed defence.
But the home striker did the trick two minutes later when he was just a yard off the line to lash a shot into the roof of the net after Hull keeper Matt Duke failed to hold a long-range free-kick from Gavin Strachan.
Hull threw everything forward for the last half-hour as they tried to get back into the game, but their attack was as weak as it had been all game and all they could show for it was a half-hearted penalty appeal when a home defender appeared to handle in the area, a few corners, and some long-range shots that flew off target.