The home side looked ready to bank their first win in seven games before the former Port Vale striker rammed a rising drive past Ross Turnbull and into the top corner of the net.
Earlier Crewe had wasted several chances to make the game safe and substitute Luke Varney had a goal chalked off for offside.
Kevin Ellison went close to giving the visitors the lead in the ninth minute when he stretched to meet Craig Fagan's cross but Darren Moss and Chris McCready managed to scramble the ball off the line.
But Crewe edged in front in the 18th minute when Eddie Johnson pounced on a loose ball on the edge of the box and hit an instinctive half-volley into the bottom corner of the net.
Fagan levelled for Hull in the 33rd minute when he finished off at the far post after Damien Delaney had knocked back Ellison's sweeping cross.
Steve Jones was unlucky not to score in the first half. He was denied by excellent keeper Boaz Myhill after he cut in to a juicy position on the edge of the box early on and then, when Eddie Johnson knocked down Anthony Tonkin's cross towards half-time the Northern Ireland international striker was denied by a timely block from Leon Cort.
But Crewe went in front five minutes before the break when Gary Roberts turned in a simple finish at the far post after David Vaughan had cut the ball back across the goalmouth.
Both sides had chances in the second half but Crewe will rue missing theirs the most. And after Paynter had equalised, Stuart Elliott came close to winning the game for Peter Taylor's outfit but was denied by a fine block from Turnbull.