In the proverbial game of two halves, the Yellows just couldn’t overturn a 2-0 half time deficit despite a host of chances and a disallowed goal in the dying minutes.
Adam Hughes’ well-struck free-kick had given the Yellows hope 16 minutes from time after Sean Cooke and Joe Mwasile put Nantwich in command.
Without skipper Mark Roberts through illness and goalkeeper Tony McMillan still sidelined with the injury he sustained last week in the FA Cup, the Yellows got off to a nightmare start in bizarre circumstances.
Robbie Evans conceded a free-kick 25 yards out from goal, and as Charlie Albinson lined up his wall against the post, Cooke placed the ball in the vacant opposite corner with just five minutes on the clock.
Nantwich were getting far too much room in midfield and a weaving run by James Lawrie resulted in him striking a shot well over the bar.
An unorthodox effort by Steve Jones, who hooked a ball over his head that came back off the top of the crossbar and then Cooke’s follow-up shot was charged down.
The hosts struck a deserved second goal on 37 minutes and it was former Yellows midfielder Joe Mwasile, who got at Alex Whittle and then swerved a shot with the outside of his right foot in to the corner with Albinson unsighted.
If the first half had been a dour display by the Yellows, the second half was the polar opposite and though boss Paul Carden will have been disappointed with the defeat, he will have been encouraged by the response of his players against a promotion rival.
They should have got back in the game within three minutes of the restart when Bohan Dixon linked up with Tony Gray to find Ben Garrity, who blazed over from just six yards out.
Largely anonymous in the first half, Gray started to pull the strings playing in a withdrawn role and he turned left-back Alex Morgan inside out before shooting over the bar.
The introduction of Dylan Vassallo gave the Yellows more impetus, but Nantwich survived the initial flurry and time ticked by.
Warrington finally got the goal their efforts deserved when Hughes stepped up to hammer home a free-kick from 25 yards and it was game on at 2-1.
Another substitute, Dominic Reid, curled a shot just wide before a superb ball by Vassallo sent Dixon away on the right and his cross was poked agonisingly wide by Gray.
The Yellows were throwing everything at Nantwich and Dixon mishit a glorious opportunity from Mitch Duggan’s cross as the hosts box was peppered in the final 10 minutes.
Garrity had big calls for a penalty turned down before the Yellows did get the ball in the net through Reid, only for it be ruled out by the assistant referee’s offside flag, and Nantwich just about held on.
Warrington, now five without a win in all competitions, are back in league action on Saturday at Grantham Town.
Nantwich Town: Spiess, Phillips, Morgan, Stair, Mullarkey, Bell, Mwasile (McDonald), Lawrie, Jones (Malkin), Cooke, Lindfield (Cotterell). Unused subs: Saunders, Glover.
Warrington Town: Albinson, Duggan, Whittle, Garrity, Raven, Hughes, Mackreth (Vassallo), Evans (Reid), Gray, Dixon, Kirby (Amis). Unused subs: Benjamin, Carden.
Pictures John Hopkins