David Fernandez looked to have set the Rugby Park hosts on their way to three points when he put the home side in front after 57 minutes.
But Gretna defender Craig Barr grabbed an equaliser 17 minutes later to earn the visitors a point, nudging them closer to a double-figures total at the foot of the table.
They now have nine points, having been docked 10 for going into administration.
Kilmarnock manager Jim Jefferies made three changes to the side beaten at Inverness last weekend as he looked for a reaction from his players.
Defender Simon Ford returned to the starting line-up for the first time in almost two months while Paul Dalglish made his first start for the club and Scotland Under-21 international Jamie Hamill was promoted from the bench.
Kilmarnock target Gavin Skelton was in a Gretna side who were seeking their second win over Jefferies' troops in the Clydesdale Bank Premier League this season, having won 4-2 at Fir Park in February, a match in which the minnows had led 4-0.
Gretna began brightly and won a corner in the second minute, but Alan Combe made an easy catch from John Paul Kissock's cross.
Kilmarnock then threatened with an Iain Flannigan free-kick from the corner of the penalty area but the Gretna defence cleared the danger.
Hamill then looked to set up Danny Invincibile and picked out the Australian in the box, but the striker could not direct his header on target.
Killie's Irish defender Tim Clancy was taken off by stretcher after 16 minutes having appeared to catch his studs on the turf. He was replaced from the bench by Grant Murray.
Flannigan should have put Kilmarnock ahead in the 21st minute when he failed to net after going clear on goalkeeper Artur Krysiak, having been set up by Garry Hay.
Kilmarnock had another scoring opportunity after 28 minutes when they were awarded a free-kick 20 yards out from goal, but Flannigan blasted the ball high into the stand.
A minute later Invincibile headed Hay's free-kick from the left flank wide of Krysiak's goal.
Invincibile again came close with a shot which was just off target, but Gretna were still in the game.
Gretna defender Kyle Naughton almost opened the scoring after 34 minutes when his shot deflected wide of Combe's post.
Krysiak pulled off a good save from David Lilley's header in the 41st minute to keep the sides level at the break.
Two minutes after the restart it took another good stop from Krysiak to deny Invincibile from scoring with a close-range header.
Barr put his goalkeeper under pressure with a pass-back after 50 minutes with Krysiak doing well to clear under pressure from Hamill.
With Kilmarnock continuing to push forward, Grant Murray headed across the Gretna goal but there was no-one in the vicinity to convert the chance.
But the Ayrshire side eventually broke the deadlock shortly before the hour mark with a well crafted goal.
Invincibile ran to the line and his cut-back was met by Flannigan, and when his shot was parried by Krysiak, Fernandez was on the spot to fire home the rebound.
Invincibile almost doubled Kilmarnock's lead after 65 minutes when he was only inches away from getting on the end of Flannigan's free-kick.
It was the visitors who were next to net with an equalising goal in the 74th minute.
Skelton's corner from the right was met by Barr and when his header came back off the woodwork he was handily placed to fire in the rebound.
Gretna, lifted by their goal and the backing of their 105 fans, made a late push for a winner against a disappointing Killie side.
But it took a good stop by Krysiak in stoppage-time to keep out Invincibile and deny Killie a win they would not have deserved.