Chester were beaten for a third successive away match as a stoppage time Lewis Maloney free kick sealed the points for the Seadogs.
The midfielder stepped up in the 94th minute to score the winner, and further late drama saw Wyll Stanway save a Michael Coulson penalty in the 96th minute which followed a Harrison Burke straight red card for handball on the line.
Calum McIntyre made four changes from the defeat at Banbury. Kevin Roberts made his maiden appearance of the season back from injury, while skipper George Glendon made his first start since May 2022.
Frankie Maguire and Matty Williams completed the quartet of changes – as Lewis Earl, Elliott Whitehouse and Zak Goodson dropped to the bench. Liam Edwards missed out due to injury.
The first half chance fell to Iwan Murray on three minutes, his snapshot following a bout of ‘head tennis’ was wide of the post.
Down the other end and the returning Roberts did brilliantly to deny Luca Colville who had controlled a cross from ex-Blue Alex Brown and shot – but the midfielder got there in the nick of time to block.
Scarborough further applied pressure and went close on 20 minutes as Dom Tear headed just wide from Lewis Maloney’s free kick.
Chester had a decent opportunity just prior to the half hour mark as Ollie Heywood sent in an awkward deep cross which found Glendon, his header was deflected behind by Cracknell.
Roberts was at it again with a crucial block on 36 minutes as a long throw found its way to Curtis Durose, his shot beat Stanway but not the Blues midfielder.
The visitors had the final meaningful chance of the half as Roberts released the pace and power of Kieran Coates who tested Cracknell with his low attempt.
It took until the 62nd minute for a first chance of the second 45 as sub Whitehouse swung in a cross which Kole Hall headed against the crossbar and over.
Scarborough’s first opportunity of the half came on 71 minutes as the hosts broke forward down the left with promising and Tear nudged inches wide after evading the challenge of Coates.
As the ending approached Chester once again had a good chance as Hall fired in a powerful effort which was beaten away by Cracknell.
But there was heartbreak right at the end as free-kick expert Maloney stepped up and curled in a beauty to win the game.
There was still time for further drama as sub Coulson broke late on and rounded Stanway before seeing his shot blocked on the line by Burke – and the Referee pointed to the spot and showed the young defender a straight red card.
Stanway though did deny Coulson from the spot with his legs in what proved to be the final action of the afternoon.
Chester: Stanway, Coates, Williams, Burke, Heywood, Roberts, Weeks, Glendon (Evans 76), Murray (Whitehouse 59), Maguire, Hall.
Subs Not Used: Goodson, Earl, Daly.
Scorer: Maloney 90+4.
Attendance: 1,815 (233 Chester).