The injury-ravaged hosts suffered a pre-match blow when defender Tim Clancy was sent home suffering from 'flu.
And manager Jim Jefferies was forced to field midfielder James Fowler in central defence alongside 20-year-old Ryan O'Leary.
It was Skelton who gave Gretna a surprise lead after five minutes when his low shot beat goalkeeper Alan Combe.
Killie came close to equalising when both Gary Wales and Fernandez were inches away from Jamie Hamill's drive across the front of Gretna's goal.
Colin Nish also missed an opportunity in front of goal from a pass delivered by Gary Wales.
Fleming did well to block a Fernandez shot at the post, but Gretna came close to doubling their lead after 20 minutes, when Deuchar's lob came back off the face of the crossbar.
Kilmarnock had another escape minutes later when Grainger's 30-yard free-kick clattered the upright.
But Killie at long last gave their fans something to cheer by equalising in the 27th minute.
Gary Locke's cross found Danny Invincibile, who swept the ball over the line from a couple of yards.
Gretna responded with a run and cross on the right from David Cowan, with O'Leary almost heading an own goal.
Kilmarnock hit back and almost snatched a late first-half goal when Wales connected poorly with a Hamill cross and failed to find the net from four yards.
Makinwa sent a free-kick just wide but won the penalty from which Gretna ahead five minutes after the break.
The referee pointed to the spot when the forward clashed heads with O'Leary and Grainger fired home from the penalty spot.
But the lead lasted just a minute, David Fernandez (right) firing home from 12 yards.
Gretna restored their lead almost as quickly, Deuchar being allowed too much time to deliver a cross into the box and Horwood curled the ball home.
Colin Nish then squandered a chance when he was through on goal, but Fleming saved well from the Killie striker.
Nish looked fortunate to escape calls for a penalty when he appeared to tug Chris Innes' shirt in the Killie penalty box.
And Fleming saved well from an Invincibile drive as the play flowed from end to end.
But Killie equalised when sub Wullie Gibson's
cross was missed by Nish but found itself into the
Sandy's Match Pic's are HERE