Substitute Jack Mackreth kept his cool to slot home in the third minute of added on time to pinch a deserved three points.
They had led early through Jack Dunn before a mistake by goalkeeper Charlie Albinson enabled Witton to equalise on the stroke of half time.
And just as it looked like the Yellows’ dominance would be in vain, Mackreth popped up to score the winner, just moments after Evan Gumbs had received a controversial red card.
After Saturday’s late show against Buxton, Paul Carden made a number of changes to his starting line-up, with matchwinner Dominic Reid preferred from the start along with striker Connor McCarthy, while Gumbs came in for his second Yellows debut.
Reid and McCarthy were involved in creating the game’s opening goal on eight minutes, working the ball nicely around the edge of the box and Dunn’s well-struck left footed shot was too strong for the ‘keeper to keep out.
It was an open Boxing Day derby with the Yellows having the better of the play, Reid shooting over after good work by the industrious McCarthy.
McCarthy almost doubled the lead shortly after the half hour mark, releasing Adam Hughes down the left and then getting in to the box to get on the end of the subsequent cross, forcing a fine save from Greg Hall at full stretch.
That prompted a spell of sustained pressure for the Yellows, and Ben Garrity thudded a header against the crossbar as the Witton goal led a charmed life.
But from nowhere, the sides would go in level at the break.
Yellows ‘keeper Albinson called for a loose ball and made a mess of it, enabling Rob Hopley to dart in and the ‘keeper then brought him down for a clear penalty, with the on-loan Blackburn ‘keeper perhaps fortunate not to have at least been yellow carded, though Dave Raven had got back to cover on the line.
James Foley stepped up to send Albinson the wrong way from the spot and it was 1-1 at half time.
Though the Yellows would enjoy plenty of the ball in the second half, they struggled to create goalscoring opportunities, and as time went on, Witton started to have openings at the other end.
Foley should have done better when a loose ball fell to him in the box, before Cesaire Lingouba’s shot was deflected wide by Raven.
With three minutes to go, a wicked Dunn free-kick came off the crossbar, the closest the Yellows had been, and fell kindly for the ‘keeper.
The game got heated in the closing stages, Gumbs shown a straight red despite clearly winning the ball, the referee determining the Tranmere man had left the ground, a decision that will cost Warrington his services for three games.
Tempers threatened to boil over in the respective dugouts but it would be a sweet ending for the visitors, Mackreth springing the offside trap and then slotting past the ‘keeper to lift the Yellows up to third in the table.
Witton Albion: Hall, Gardner, Devine, Wardle, Humphreys, Lussey (Lingouba), Smart, Owens, Hopley, Jones, Foley. Unused subs: Booth, Yates, Cobley.
Warrington Town: Albinson, Duggan, Hughes, Gumbs, Roberts, Raven, Reid (Mackreth), Garrity, McCarthy (Amis), Dixon (Vassallo), Dunn. Unused subs: Evans, Gray.