Chester lost for the first time at home this season, conceding two late goals at the Leap76 Stadium.
Declan Weeks’ penalty had put the Blues a goal to the good at half time – but late strikes from Lassana Mendes and then Aurio Texieria gave the Bulls all three points.
Calum McIntyre made three changes from Saturday. Harrison Burke and Kole Hall returned to the squad, and Frankie Maguire started. They replaced Liam Edwards, Iwan Murray and Connor Evans – who all dropped to the bench.
The Blues had the first chance after a quiet start, as Maguire and Hall combined, the latter seeing his low effort saved and held by Curtis Pond.
Ollie Heywood created the next opportunity, a progressive run towards the Hereford box, and his cutback seemed to just take a bobble which meant Hall blazed well over.
There was little for discussion at the other end, as a Kian Ryley cross was glanced wide by Alex Babos.
Then on 34 minutes Chester were awarded a spot kick by Referee Luis Griffiths.
Burke played a superb ball out wide to Kieran Coates, who controlled with equal excellent measure before driving towards the box and being tripped by Adam Livingstone.
Weeks stepped up and confidently potted the ball into the corner, despite Pond guessing the right way.
One was nearly two before the half was out. Weeks’ corner found Hall, his deflected effort fell into the path of Kev Roberts, who saw his shot somehow blocked on the goal line from a few yards out.
The Bulls responded just after the break as loanee Sonny Singh dragged a low effort just wide on 50 minutes.
Down the other end Chester started to build some pressure with a succession of corners – one was punched unconvincingly by Pond and Whitehouse’s shot deflected inches wide.
Hereford had an opening midway through the second 45 as Stanway failed to hold on to Livingstone’s cross, but sub Connor Stanley volleyed off target.
Nevertheless the Bulls won it with a double salvo late on.
Their pressure continued to build as the half progressed, and reached a climax when a deep cross found its way to sub Mendes who fired beyond Stanway at the near post.
Then on 88 minutes they struck the winner – a cruel blow – as Texieria let fly and scored with an incredible 30 yard thunderbolt from range.
Chester: Stanway, Coates, Burke, Williams, Heywood, Roberts, Glendon (Murray 50), Weeks, Whitehouse, Maguire (Caton 61), Hall.
Subs Not Used: Evans, Sparrow, Edwards.
Scorers: Weeks (pen) 35; Mendes 84, Teixeria 88