Player-manager Paul Merson, who otherwise had an indifferent match, suddenly produced a brilliant 85th minute flick on which paved the way for Fryatt to stroke home his 14th goal of the season.
It was a game of few clear-cut chances, but Walsall had the better of them.
In the second minute a chip by Daryl Taylor could have produced a goal for the home side, but successive headers by Julian Bennett and Fryatt failed to find the target.
On-loan Dean McDonald, who returns to Ipswich on Monday, was Hartlepool's liveliest player.
In the ninth minute the tricky striker forced Joe Murphy into a rare save with an angled shot.
There was a blow for Hartlepool after 15 minutes when skipper Michael Barron had to go off injured to be replaced by Darren Williams.
After Hartlepool had looked the better side in the early stages, Walsall suddenly sprang into life when a fine free-kick by Merson in the 25th minute was well turned over by Dimitrios Konstantopoulos.
The Hartlepool keeper produced another fine save two minutes later from a shot by young Walsall striker Alex Nicholls.
Hartlepool's best chance fell to McDonald a minute after the interval, but he drove just wide following a good headed flick-on by Chris Llewellyn.
Chances during the second half were rare, but Taylor had a shot saved by Konstantopoulos in the 62nd minute and namesake Kris Taylor shot just over from 25 yards after 70 minutes.
It looked as though the game was going to peter out into a goalless draw when that great combination from Merson and Fryatt produced a victory which Walsall just about deserved.