Gallacher was called into action again when David Silva tried his luck from distance, the keeper doing well to push the ball out for a corner.
Dayton's deliveries into the penalty area were causing the visitors problems, but neither Frazer Wright or Manuel Pascali could make a clean connection from the winger's corner after 15 minutes.
And another Dayton corner two minutes later was headed over by Mohamadou Sissoko.
St Mirren ventured up-field and won a corner, from which Hugh Murray headed over, and within minutes the Buddies had fallen behind.
Jamie Hamill found Dayton on the flank and the former Crystal Palace player cut inside to send a left-foot shot into the top corner.
Injury ended Silva's match after 38 minutes and his replacement, Harry Forrester, fired a shot beyond the post in the closing minutes of the first half.
Having rarely threatened before the interval, St Mirren unexpectedly levelled in the 48th minute as Killie failed to deal with a bouncing ball and Thomson took full advantage by slamming a low shot into the net from close range.
A foul by Marc McAusland on Bryson gave the home side the chance to regain the advantage and Eremenko successfully converted the set piece chance with a curling low shot.
There was another injury blow for Kilmarnock when Dayton had to be replaced with James Fowler following a challenge by Jure Travner.
McGowan was red carded following an apparent off-the-ball altercation with Manuel Pascali, which occurred in the aftermath of Dayton's injury.
St Mirren substitute Sean Lynch was denied a second equaliser by Kilmarnock goalkeeper Cammy Bell.
Forrester was a persistent threat to the visiting defence throughout the second half and forced Gallacher into a save after finding space to get in a shot.
A late charge by St Mirren created a chance for Gareth Wardlaw, but Bell was equal to the shot to ensure Killie finished as winners.
Kilmarnock Bell, Hamill, Wright, Sissoko, Gordon, Silva (Forrester 38), Bryson, Pascali, Dayton (Fowler 65), Sammon, Eremenko.
Subs Not Used: Letheren, Clancy, Hay, Invincibile, Kelly.
Booked: Hamill.
Sandy's Match Pic's are HERE