CENTRE back George Horan proved the hero of a magical finale for the Blues.
The defender headed an injury time winner from Iain Howard’s corner to secure a memorable three points against their plucky hosts.
Striker Michael Wilde and midfielder Bradley Barnes had scored the Blues goals either side of half-time to earn the club a 2-0 lead.
Injury time replies by Dave MacPherson and Ashley Stott put Witton back on level terms to set up a frantic finish.
But Horan had the final word and wheeled away with both arms in the air in celebration to cap a superb never-say-die display.
The victory hoisted Chester to third position in the Division One North league table and put the club's hopes of challenging for promotion back on track.
Chester were rarely troubled by an Albion side throughout the game who saw their run of six unbeaten league games come to an abrupt end.
Blues boss Neil Young made three changes to the side that was held 1-1 at home by Prescot Cables at the weekend. Defender Stuart Jones, midfielders Tom Field, and Howard, started in place of Andy Burgess, Greg Stones, and Rob Hopley.
Chester started the brightest and forced a corner taken by Chris Williams in the opening minute which Witton defender Ben Harrison did well to head clear.
Chris Williams demonstrated his pace and trickery on the left flank a minute later and picked out Iain Howard with a low pass, but Howard's 10 yard shot was smothered by home keeper, Matt Cooper.
Chester looked in control and so nearly broke the deadlock in the 10th minute when Tom Field worked his way into space and unleashed a 25-yard shot which Cooper pushed wide of his right post.
The Blues were forced into making a substitution seconds later when midfielder Burgess replaced Mark Connolly who was clearly struggling with a knock he had picked up from a late tackle.
Witton offered very little against a lively Chester side, but they constructed their first effort on goal after 17 minutes when Dave MacPherson's low 25 yard attempt flew harmlessly wide of the right post.
The Blues did find the target in the 22nd minute when Robbie Booth's left-sided corner found Barnes whose effort was parried by Cooper into the path of Wilde who made no mistake from close range.
Left sided Albion midfielder Callum Botham was then offered two dubious free kicks on the edge of the Chester area. His first was fired into the sidenetting, and his second was hoisted well over the target.
Williams showed a clean pair of heels to his marker on the left flank in the 34th minute, but his cross into the box was cleared by Albion skipper Ian Kearney.
Booth tried to increase the pressure on their hosts five minutes before the break with a run and cross from the right which Cooper had to tip clear at full stretch.
And the half concluded with a Witton free kick, but Andy Kinsey's 22 yard attempt was ballooned well over the mark.
Booth was teed up by Howard in the 50th minute as Chester retained command of the contest, but the striker opted to take a touch rather than shoot from the edge of the box and the ball was whipped from his feet by Matthew Holt.
Chester were denied a chance to increase their advantage in the 55th minute when Williams' corner was headed goalwards by George Horan, but defender Matthew Wood was perfectly placed to clear the ball off the line.
Witton responded with two successive corners, the first deflected wide from striker Stott's head, and the second resulting in a free kick for a foul on Blues keeper, Richard Whiteside.
Chester doubled their goal tally for the night after 58 minutes when Whiteside's long kick was flicked on by Booth and then to Barnes who drilled a sweet 25-yard shot beyond Cooper and into the bottom left corner of the net.
Barnes was then presented with a fine chance to extend the Blues advantage six minutes later, but his close range shot from Booth's incisive pass was pushed wide of the right post by Cooper.
Centre half Ruffer, was gifted a free header from Williams' right-sided corner seconds later, but his eight yard effort was gratefully gathered by Cooper.
Blues fans' elation turned to frustration with the match officials minutes later as two perfect looking attacks were pulled back due to raised offside flags.
Howard continued the dominant Chester display with a powerful run and cross from the left which Booth steered wide with his head.
Tom Field steered a 78th minute free kick over the bar as Chester continued to press for a further opening.
Booth constructed the next attack and fed Barnes who audacious overhead kick bounced wide of the right post from 15 yards.
Kyle Wilson made his Chester debut as an 86th minute substitute in place of Booth as the Blues injected fresh legs into their forward line.
Chester were stunned in the dying minutes when MacPherson and Stott both pulled Witton back on level terms. But Horan had the last word in the fourth minute of injury time when he headed home.
WITTON ALBION (4-4-2): Cooper; Holt (Pritchard 65), Wood, Harrison, Kearney, Maguire, Griggs (Frost 55), MacPherson, Stott; Kinsey (Pugh 72), Botham. Subs (not used): Jones, Moffatt.
CHESTER (4-3-3): Whiteside; Jones, Ruffer, Horan, Williams; Field (Hopley 90), Barnes, Connolly (Burgess 10); Howard, Wilde, Booth (Wilson 86). Subs (not used): Peers, Wilson, Graves.
Referee: Gary Hilton (Upholland, Lancashire).
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