Chester were forced to play the majority of the game a man short having lost midfielder Ricky Ravenhill after only 25 minutes, and the numbers were levelled 13 minutes from time when Steve Evans also saw red.
The visitors had threatened early on with Matt Done being denied by a brilliant block from Chester captain Steven Vaughan, who had tracked all the way back.
From the resulting corner Evans sent a header just wide of the post. At the other end Paul Linwood powered a header which was cleared off the line by Ryan Valentine.
The game exploded into life when Ravenhill, making his debut for the Blues, was controversially sent off by Premiership referee Uriah Rennie.
Wrexham keeper Michael Ingham had come out of his box to deal with a bouncing ball, chested it down, and then appeared to handle outside his area before he was clattered into by Ravenhill.
The numerical advantage saw Wrexham start to impose themselves on the game, and Done hit a good opportunity wide, before Mark Jones fired a volley just past the post five minutes from the interval.
The visitors were then awarded a penalty two minutes later when another foraging run by Done was brought to an end by a clumsy challenge from Vaughan.
Captain Neil Roberts made no mistake from the spot, sending goalkeeper John Danby the wrong way to make it 1-0.
Chester made a change at the break with Simon Marples coming on in place of Ashley Westwood and they went close when Laurence Wilson stole the ball but fired straight at keeper Ingham.
But it was Chester who fell further behind on 52 minutes when a delightful ball from Steve Evans played in Mark Jones, who made no mistake in lofting the ball over Danby.
The home side refused to lay down and die. And they were given hope when Wrexham were also reduced to ten men 13 minutes from time when Evans was dismissed for his second bookable offence.
Jamie Hand managed to pull one back for the Blues on 81 minutes when he hit a thunderous shot from outside the box into the bottom corner, but it proved only a consolation as Wrexham held on for the win.