The St Johnstone substitute drilled home a diagonal effort four minutes from time to cancel out Conor Sammon's first-half opener for the hosts from an Alexei Eremenko free kick.
Kilmarnock dominated the first half at Rugby Park and could easily have been further in front before the break after further opportunities for Garry Hay and Sammon in particular.
However, the second half was a much more even affair with Saints having the better chances in front of goal.
Kilmarnock's new signings, midfielder Benjamin Laurent and defender Billy Berntsson had to settle for places on the bench.
Home manager Mixu Paatelainen made just two enforced changes following the Ayrshire side's Scottish Cup defeat at Ibrox last Monday - James Fowler and Tim Clancy started in place of the injured Craig Bryson and suspended Jamie Hamill.
Peter MacDonald, who came off the bench to net St Johnstone's late winner in their midweek Scottish Cup tie at Hearts, was rewarded with a starting place for the visitors, swapping places with Sam Parkin, who was among the substitutes' ranks.
Kilmarnock earned a corner in the first minute, and although Alexei Eremenko's delivery from the left was cleared, it set the tone for an entertaining opening period.
Mehdi Taouil was particularly lively on the hosts' left wing, and David MacKay made an important clearance in the six-yard box on 10 minutes when an Eremenko cross from the right looked destined to arrive perfectly for Liam Kelly.
At the other end, MacDonald had St Johnstone's first real chance when he sent a diving diagonal header well wide of the left-hand post.
Kilmarnock took a deserved lead on 16 minutes with a clever, well-worked goal from the training ground after Kelly had been brought down for a free kick.
Eremenko stood over the set piece, towards the left flank, and bypassed the visiting defence by slipping it neatly up the line for the anticipating Sammon, who slid a neat close-range finish low into Peter Enckelman's net.
Kilmarnock remained in the ascendancy with Sammon and Taouil regularly bearing down on goal.
Enckelman had to look smart to rush out and scoop the ball to safety on 27 minutes after another impressive Kilmarnock move starting with an Eremenko back-heel to Tim Clancy, advancing at pace from right-back.
Michael Duberry did well to intercept a Taouil pass intended for well-positioned Sammon on the half-hour, and visiting goalkeeper Enckelman then made two important saves just moments apart.
First he caught the ball at the left-hand post to prevent Hay doubling his side's lead by meeting Eremenko's precise long cross from the right with a good header.
Enckelman then stopped Sammon making it 2-0 after the striker beat Duberry to latch onto a fantastic Taouil pass from inside his own half and strode in on goal, only for the goalkeeper to smother it on the six-yard line.
The hosts were well in control - but almost saw Samuel equalise two minutes from the break with a rising shot which home goalkeeper Cammy Bell stretched to tip over the bar.
The second half got underway with some meaty challenges although only one booking, Eremenko and Jody Morris taking particular exception after a clash on the left touchline which had the duo bickering for several moments even after the intervention of referee Steven McLean.
MacDonald came agonisingly close to an equaliser for St Johnstone eight minutes after the restart, but put his glancing header from Danny Grainger's corner narrowly wide of the opposite post.
Grainger then took a free kick from just outside the box, but his effort sailed harmlessly well over the bar.
St Johnstone enjoyed far more possession and goal attempts in a more even second half, but without seriously troubling Bell in the home goal.
Sammon then squandered a good opportunity as the game entered its final quarter, Taouil skipping past Duberry on the halfway line to put the striker clear, only for him to pull his shot well wide.
The visitors introduced forward Cleveland Taylor for the final 20 minutes and pressed hard for an equaliser but without being able to capitalise on a number of free kicks and corners.
Bell was relieved only to concede a corner on 76 minutes when he was unable to control a quick close-range passback from Mohamadou Sissoko in the miserable and constantly blustery conditions.
The home goalkeeper reacted well to push away a close-range header from Murray Davidson eight minutes from time - and immediately at the other end, Enckelman was called into action to stop a Sammon effort.
However, four minutes from time, St Johnstone earned the equaliser which the second-half showings had merited when Taylor ran onto a ball down the right wing and was able to slot home a drilled effort which nestled in the opposite corner of the net.
Berntsson made a late debut for the hosts with two minutes left.