Just 90 seconds after Michael Symes had successfully netted from the spot to secure Shrewsbury the points, referee Lee Probert blew for time. Rival players and officials immediately became embroiled in a series of touchline brawls that resulted in Town skipper Sagi Burton being shown a red card.
More altercations followed and there was a further clash in the tunnel as the opposing factions headed for the dressing rooms.
Town manager Gary Peters called the incidents regrettable and said he would study video evidence before commenting.
There had already been enough animosity in this highly charged fixture with six cautions - five of whom were Chester players - and a 16-man push and shove session early in the second half, before the controversy of the 90th minute penalty decision.
Gregg Blundell had given the visitors an early lead, before ex-Chester man Ben Davies - jeered every time he touched the ball by visiting fans - levelled for Shrewsbury five minutes after the break.
Despite dominating for long periods and going close to a winner on a number of occasions, it seemed Town would have to settle for a point but, in the final seconds of normal time, a shot from Derek Asamoah struck the arm of Chester defender Dave Artell - himself a former Shrewsbury player - at point-blank range.
But the referee had no hesitation in pointing to the spot, which enabled Symes to secure Peters' side their first league win since early October.
Blundell put Chester ahead in the eighth minute, pouncing on some hesitancy in the Shrewsbury defence to score from close range.
But for the remainder of the half most of the action was at the opposite end as Shrewsbury were often inches away from ending a four-game goal drought. Despite several near misses, particularly from young midfielder Dave Edwards, they reached the interval still without a goal to show for their efforts.
But all that ended five minutes after half-time when Davies was on hand to score from inside the six-yard box following good work from Asamoah - Shrewsbury finally breaking their duck after a barren spell of 416 minutes.
As they pressed hard for a winner, Davies had a goal disallowed, Symes found the side-netting and Edwards hit the woodwork but it appeared victory would elude them until the high drama of the closing seconds.