Hibs 11th month unbeaten league run at Easter Road came to an end in dramatic fashiion as Joe Shaugnessy claimed a goal in the final minute.
A superb penalty stop from goalkeeper Adam Bogdan appeared to have salvaged a point for the Edinburgh club, the on-loan Liverpool man getting down to push aside Danny Swanson's effort from 12 yards.
But just as it looked as if Hibs would hold on for a point Shaugnessy turned home David Wotherspoon's free-kick to inflict a first Premiership defeat on the Edinburgh club on their onw turft since Rangers last December.
Martin Boyle went close for Hibs with a rising shot which screamed just wide of target before 'Saints went even closer, Matty Kennedy playing a corner out to the unmarked Tristan Nydam lurking just outside the home side's penalty area, the oon-loan Ipswich Town youngster enjoying the space to crack in a tremendous effort which smashed back off goalkeeper Adam Bogdan's cross bar.
Compared to Wednesday night's highly charged Edinburgh derby this was, predictably, a much more sedate affair, Hibs boss Neil Lennon having been greeted with a chant of "there's only one Neil Lennon" from the home fans keen to show him their backing after the events at Tynecastle.
Clear goal-scoring opportunities at either end were at a premium, Mark Milligan coming up with a great block as Tony Watt got on the end of Drey Wright's low cross before Emerson Hyndman attempted to find the far top corner of Zander Clark's net but was well off target.
Without the suspended Flo Kamberi Hibs lacked a physical presence up-front against a Saints' side which hadn't conceded a goal in winning their three previous league matches.
But Lennon;s players brought their fans to life with two terrific efforts in the space of a minute, Clark getting his fingertips to Boyle's ferocious shot and then managing to get a hand to a swerving Mallan effort which appeared to have caught him going the wrong way.
Lewis Steveson's cross eluded everyone to find Jamie Maclaren at the back post but the Australian striker couldn't get enough on to trouble Clark.
Referee Nick Walsh had pulled up Marvin Bartley more than once for using his strength to muscle Saints players off the ball - much to the disbelief of the midfield powerhouse - and he had no hesitation in pointing to the spot when he leaned on former team-mate Swanson who had replaced Kennedy only three minutes earlier.
Swanson stepped up to take the spot-kick himself, firing the ball low and hard to Bogdan's right but the Hungarian internationalist got down superbly to push the ball round the post.
Hibs were beginning to looked tired following their midweek exertions in Gorgie, those injuries to David Gray, Paul Hanlon and Thomas Agyepong allied to Kamberi's suspension curtailing Lennon's options while Maclaren was suffering from a distinct lack of game time following his own injury problem.
Vykintas Slivka and Darren McGregor were thrown on, as was Oli Shaw, to add fresh legs as Lennon also tinkered with his line-up in an effort to get that one goal which, increasingly, looked as if it would win the game .
But just as it looked as if they'd emerge with a point came that dramatic last minute winner from Shaugnessy.
Hibs: Bogdan, Whittaker (McGregor 68), Ambrose, Milligan, Stevenson, Bartley, Mallan, Horgan (Shaw 77), Hyndman (Slivka 68), Boyle, Maclaren.
/Substitutes not used: Marciano, Mavrias, Porteous, Gullan.
St Johnstone: Clark, Forster, Shaugnessy, Kerr, Wright, Callachan, Craig, Nydam (Wotherspoon 69), Tanser, Kennedy (Swanson 63), Watt (Kane 77)
Substitutes not used: Hurst, McMillan, McCann, Gordon.
Referee: Nick Walsh