Fryatt drilled home his 12th goal of the season in the 88th minute to deal Middlesbrough's play-off hopes a blow after teenage winger Joshua King had scored his first goal for the Tigers to cancel out Marvin Emnes' first-half opener.
It was Hull's first home win since February 11 and the three points kept them in 10th place - four points behind Cardiff, who occupy the final play-off spot.
Boro have now drawn four and lost four of their last eight games, but Tony Mowbray's side remain two points better off than Hull in eighth place.
Hull boss Nick Barmby recalled five players in a bid to stop the rot. Midfielders Robert Koren, defender James Chester, striker Fryatt, plus wingers Robbie Brady and King all returned.
Middlesbrough made four changes themselves after Saturday's home defeat to Cardiff, with midfielders Richard Smallwood and Julio Arca, defender Tony McMahon and Emnes back in the side.
King forced Middlesbrough goalkeeper Jason Steele into a sprawling save with a low shot from inside the penalty area in the fourth minute.
Brady then saw his 20-yard drive blocked by Stephen McManus, but Boro made the breakthrough with their first noteworthy effort in the 13th minute.
Midfielder Nicky Bailey crossed from the right and, when the ball broke to Emnes on the left side of the area, the Dutchman curled a right-footed shot into the top corner.
Encouraged by his 17th goal of the season, Emnes went close to making it 2-0 to Boro in the 31st minute, but Hull goalkeeper Vito Mannone saved smartly to keep out his angled shot.
Fryatt had another shot charged down, but otherwise Hull laboured to get back on terms before the break.
Barmby's side bossed possession after the restart and scored their first goal in over four and a half hours at the KC Stadium when King rifled home a loose ball in the penalty area high into the net in the 58th minute.
The Tigers were now in the ascendancy and Richard Garcia, operating in the back four due to Liam Rosenior's injury, volleyed straight at Steele from 20 yards.
Despite being under the cosh for long periods, Boro served warning of their capabilities on the break when striker Scott McDonald headed McMahon's deep cross just off target in the 73rd minute.
Boro boss Mowbray sent on striker Bart Ogbeche for Emnes and winger Adam Hammill for Arca with 16 minutes left before Brady fired a long-range shot wide as Hull went in search of the winner.
Fryatt's volley from inside the area was blocked by McManus and Tigers substitute Cameron Stewart's thumping shot was well saved at full stretch by Steele.
McManus headed over the crossbar for Boro, but with the clock running down, King supplied the cross from the right and Fryatt reacted quickest to arrow a shot into the bottom corner.