Gate suffered their second Hallmark Security League defeat in five days after conceding an agonising 90th-minute winner in east Lancashire.
Only one point separated these mid-table premier division sides at start of play and Gate made two changes to the team beaten at home by Barnton on Saturday, with Ryan Stayte and Joe Noblet coming in for Andrew Richards and Ryan Riley.
This was an altogether tighter game than last month’s encounter at Marton, which Padiham won 4-1, and there were very few chances for either side in the first half.
Padiham’s Michael Donlon was the busier goalkeeper, punching clear to prevent a Gate corner reaching the head of former Storks player Seydou Bamba.
Donlon then had a nervy moment under pressure from Brett Dawson but he recovered to ensure the half ended goalless.
The teams continued to cancel each other out for much of the second half, though Dawson did fire a rare shot the wrong side of the post eight minutes in.
Noblet steered a free-kick just wide following a foul on the edge of the box but Gate’s best chance fell to Dawson.
He was sent clear by fellow frontman Ric Seear but Donlan got down well to save Dawson’s strike low to his right.
A draw would have been the fair result result but home striker James Dean, a scorer at Gate last month, had other ideas.
He poked the ball home in a goalmouth scramble to condemn Gate to a last-gasp defeat which drops them to 14th.
They will be anxious to return to winning ways at second-bottom Nelson on Saturday.
Gate: Fletcher, Stayte, Carroll, Alexander, Bamba, Hall, Thornber, Noblet, B.Seear, R.Seear, Dawson. Subs: Higham, Riley, Buchan, Tanser.