The Wolves led 26-20 at the Halliwell Jones Stadium when Jacob Wardle crashed over for the Giants to the left of the posts with just four minutes remaining, but Danny Brough missed the conversion.
Huddersfield were awarded a penalty as the hooter sounded but Brough’s last-gasp effort from the halfway line was again off target much to the relief of the home supporters.
The win sees Warrington open up an eight-point gap over the fifth-placed Giants with just three games remaining of the Super 8s before the semi-finals, when the Wolves are likely to have to travel to St Helens or Wigan to battle for a place in the Grand Final at Old Trafford on October 13.
Bryson Goodwin claimed two tries for the Wolves to make it seven in two games for the Kiwi centre, with others coming from Stefan Ratchford, Tom Lineham and Ryan Atkins with Tyrone Roberts kicking three goals.
Jake Mamo claimed a first-half hat-trick for the Giants in defeat and Lee Gaskell and Wardle also touched down, with Brough landing just two conversions.
The Wolves welcomed back Atkins after a 10-game absence following bicep surgery and Harvey Livett was recalled after missing the 80-10 win over Hull.
Huddersfield made a host of changes, with Jermaine McGillvary, Leroy Cudjoe, Darnell McIntosh, Aaron Murphy and Colton Roche all missing from the side that lost 42-16 at home to Wakefield. Mamo, Wardle, Innes Senior, Oliver Roberts and Daniel Smith came in. And the Giants suffered an early blow when in the first set they lost Alex Mellor who suffered a facial injury in a challenge that was placed on report by referee James Child.
Warrington Wolves: Ratchford, Lineham, Goodwin, T. King, Charnley, K. Brown, Roberts, Hill, Clark, Cooper, Hughes, Atkins, Livett. Substitutes: Philbin, Patton, G. King, Pomeroy.
Huddersfield Giants: Rankin, Mamo, Turner, Wardle, I. Senior, Gaskell, Brough, Ta’ai, O’Brien, Matagi, Mellor, Roberts, Hinchcliffe. Substitutes: Leeming, Lawrence, Clough, Smith.
Referee: James Child (RFL)