The 25-year-old striker netted either side of the break to extend Rovers' winless streak to eight matches in the process.
Hull dominated first-half proceedings and took the lead through a Richard Garcia tap-in, although the visitors equalised seven minutes later through Franck Moussa.
However, Fryatt secured victory for the home side by smashing home a 21st-minute penalty before heading home at the back post shortly after the restart.
Rovers had the bulk of possession in the second period and fought valiantly to reduce the deficit, but goalkeeper Vito Mannone and his defence kept the visitors at bay.
Despite a promising start from the visitors, their defensive fragility was evident from the outset.
First goalkeeper Gary Woods was forced to save well from a close-range Fryatt effort, before Robert Koren flashed a shot across the face of the goal.
However, Rovers' resistance lasted just nine minutes as they conceded their 73rd goal of the season.
Great play from the Tigers resulted in Fryatt breaking free in the box and when his scuffed shot was palmed across the goal by Woods, winger Garcia was on hand to slot home.
While Doncaster were on the back foot, they looked dangerous on the break and managed to draw level just seven minutes after going behind.
James Coppinger's long-range drive ricocheted back off the post and Moussa pounced on the rebound to fire home.
However, in a frenetic start to the game Shelton Martis handed the home side an opportunity to equalise by giving away a penalty for up-ending Corry Evans in the box.
Fryatt stepped up to take the spot-kick and finished with aplomb, thumping the ball into the bottom left-hand corner past the outstretched arm of Woods.
The former Leicester striker's goal handed Hull the impetus again, with Koren flashing a shot wide, Garcia heading over and James Harper curling a shot just wide in the moments that followed.
While Hull headed into the break with a comfortable advantage, the first half was tempered somewhat by a serious-looking injury that forced Garcia off on a stretcher.
Jamie Devitt came on for the Australian in the 41st minute and played an integral part in Hull's third of the afternoon just after the break.
The Irish winger broke free down the right and neatly pulled the ball back at the byline to Liam Rosenior, whose cross was met at the far post by a stooping header from Fryatt.
The goal seemed to spur the visitors into life, though, with Coppinger, Simon Gillett and James Hayter all thwarted in their bid to reduce the deficit.
Hull still looked lively in attack but spent most of the second period camped in their own half, with Mannone pulling of a string of saves to prevent Rovers pulling one back.
As the game petered out fans were treated to one of the misses of the season from substitute Aaron Mclean, who somehow managed to scuff wide unmarked in the six-yard box with the goal beckoning.