Paul McManus' header after 23 minutes proved the decisive moment for the tenacious home side on a blustery night in Cheshire.
With a light rain swirling around in the wind, conditions weren't condusive for passing football and the home side snapped away, refusing to let us settle into any pattern. That led to us forcing the issue on a couple of occasions and potential moves breaking down - a frustrating first half.
Still, goalmouth action was at a premium at both ends and it took until the 14th minute for the first effort at goal, Thorpe's half-volley straight at Button.
Using diagonal balls from all angles, Chester gained good territorial advantage and it paid off in the 23rd minute when Newton swung in a fine cross from the left touchline, picking out McManus, unmarked, eight yards out. He planted his header beyond the diving Button.
A couple of corners caused minor panic in the home defence as the half wore on and our best moment of the half arrived in added time as Pekhart won a 50-50 centrally and played in Fraser-Allen down the right, he drove in a fierce cross-shot that Vernon took well low down to his right.
Alex Inglethorpe rung the changes at half-time. Takura Mtandari made way for Andros Townsend, who joined Pekhart and Hutton up front in a 4-3-3 system. Hughton switched to right-back, Martin to left-back and Archibald-Henville to centre-back alongside Casey.
That move certainly led to us enjoying more possession and the ball was finally being popped around in a more measured fashion. The tempo also shifted a gear - but although they were clearly tiring, Chester remained tight as a unit and chances remained scarce.
Hutton had Vernon scrambling to his right as his free-kick curled just wide but it was Button in action next, the keeper forced to palm Newton's inswinging corner off his goal-line before a more routine save from McManus, 70 minutes on the clock.
It always looked like it would be a case of taking that one chance that fell our way and it arrived after 75 minutes. Hutton curled in another free-kick, this time from the right and Archibald-Henville rose high, made contact only to see his header glance agonsingly wide.
Try as we might, we couldn't carve out another opportunity as Chester held on.
THE KEY ACTION...
14mins: First effort on goal from either side, Thorpe decent strike on the half-volley from 20 yards hit straight at Button.
23mins: GOAL - CHESTER. Newton swung in cross from the left touchline that found McManus with a free header, eight yards out, planted it past diving Button.
Chester City 1, Spurs 0
28mins: Vernon did well to tip Hutton's inswinging corner from underneath his crossbar under pressure from Pekhart.
37mins: Tricky ball again for Vernon, did well to take at second attempt with Archibald-Henville looking for any pieces.
39mins: Thorpe drove a couple of yards wide from the edge of the box.
Added time: Our best moment yet, Pekhart won 50-50 and played in Fraser-Allen, right channel, drove in a cross shot that Vernon gathered well low to his right.
Half-time: Chester City 1, Spurs 0
49mins: Button out to pounce on loose ball at feet of Thorpe.
50mins: Townsend cross from left just evaded Pekhart at the near post.
52mins: Owen important block to keep out Martin's volley from 10 yards.
66mins: Hutton free-kick from 30 yards curled just wide.
70mins: Newton's inswinging corner almost caught out Button, keeper did well to palm off line.
70mins: McManus decent strike from 20 yards forced Button into action again, comfortable save down to his left.
73mins: CLOSE. Hutton curled in free-kick from the right, Archibald-Henville rose well but glanced header agonsingly inches wide of far post.
75mins: Combination of Pekhart and Martin up to meet Hutton's corner, ball looped wide.
Full-time: Chester City 1, Spurs 0
Chester City: Vernon, Rule (Rowlands, 65), Newton, Roberts, Kelly, Owen, Mitchell, Carroll, Thorpe (Feliciello, 53), Gregory, McManus (Morrin, 79). Subs: Robson, Brownrigg.
Spurs: Button, Mtandari (Townsend, 46), Hughton, Archibald-Henville, Martin (Smith, 75), Casey, Fraser-Allen, Livermore, Pekhart, Hutchins (Medley, 85), Hutton. Subs: Stroud.
Our Under-18s fell at the first hurdle of this season's FA Youth Cup as Chester City won Wednesday night's third round tie 1-0 at the Saunders Honda Stadium.