Padiham struggled to make any headway against Flixton on a terrible playing surface at their Valley Road ground.
The Storks never recoveted from conceding two goals in the space of three minutes just after the half hour mark in the Vodkat Premier Division fixture.
Chris Smith headed the home side in front from a corner in the 31st minute and a right-wing break from Brian Matthews then ended with the winger cutting inside and sending a shot past Padiham keeper Sean Davis to give Flixton their 2-0 winning margin.
Martin Parkes came closest to pulling a goal back when he headed against the crossbar midway through the second half.
Padiham host Ramsbottom at the Arbories on Wednesday, kick-off 7.45pm.
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