Jim Jefferies' selection dilemmas further intensified before kick-off when Tim Clancy, who had been pencilled in to play at centre-back for Kilmarnock went down with flu and was sent home, leaving James Fowler to step into the backline.
Killie's makeshift back four was all over the place early on and it was no surprise when Gretna scored in the fifth minute. Henry Makinwa shrugged off Jamie Hamill and teed up Gavin Skelton in acres of space in the box and he fired home.
Bottom club Gretna were left cursing their luck as they hit the bar twice in two minutes. First, on 21 minutes Killie keeper Alan Combe was caught in no-man's land as Kenny Deuchar chased a long ball and the returning striker lobbed the ball over him, but off the underside of the bar.
Next, Danny Grainger turned away in dismay as his brilliant free-kick smacked the woodwork. The same player was denied by Combe a minute later from another dead ball strike, but the keeper made a great save low to his right.
Gretna midfielder Allan Jenkins then struck a great 30-yarder which was only inches wide.
For all their dangerous attacking play, Gretna were vulnerable at the back and they conceded a soft equaliser in the 27th minute. The defence allowed a high ball to reach Danny Invincibile at the far post six yards out and the Australian scrambled the ball over the line.
Gretna were handed the opportunity to re-take the lead when referee Chris Boyle awarded them a controversial spot-kick after an accidental clash of heads between Ryan O'Leary and Makinwa. Grainger ignored the furore and smashed the ball home.
Again Gretna could not hold the lead and Killie were level four minutes later after another defensive mistake. Hamill sent a beautiful cross into the middle, but Greg Fleming punched then ball against Colin Nish and into the path of David Fernandez, who made no mistake.
It was a pulsating match, with the home fans convinced they were getting a raw deal from the referee, but their defenders switched off in the 57th minute to go behind for the third time in the game.
Evan Horwood had all the time he needed at the edge of the box to measure a nice curling shot into Combe's right corner.
Killie refused to give in and substitute Willie Gibson danced inside his marker to fire over a low cross which appeared to take a slight touch off Nish before finding its way inside the far post.