The match had appeared destined to end in stalemate when deep in added time, a mix-up between Ashley Westwood and keeper John Danby, who left to ball to one another, allowed Gary Jones to nip in and open the scoring.
This was followed almost immediately by a second goal when Andy Taylor beat the offside trap to coolly side foot the ball into the net.
Up until that point, chances had been few and far between, with both sides seemingly content with a point. Chester's best moment came in the fifth minute when a curling shot from Roberto Martinez appeared destined for the top corner until it was palmed away by Phil Barnes.
The Grimsby keeper was in the thick of the action two minutes later, this time producing a poor clearance which went straight to Laurence Wilson, but the Chester midfielder's shot at the unguarded goal went over the bar.
The visitors also had a lucky escape when last defender Tom Newey appeared to bring down Gregg Blundell, who would have been in on goal, but the official waved play on.
The Mariners took a while to get into their stride, but as the first half wore on they started to put more pressure on their hosts without carving out any decent opportunities as Chester defended a number of high balls into the box well.
Two minutes after the restart Grimsby were ruing their luck when a fine individual run and shot from outside the box by Peter Bore cannoned of the bar and away to safety.
A dead ball situation outside the area gave substitute Kevin Sandwith a chance to break the deadlock, and he curled an effort from 20 yards just inches past the post.
Ricky Ravenhill, who early this season was sent off on the same pitch while playing in Chester colours, went into he book for foul on Wilson.
The increasingly lively Bore looked set to run clear on goal when he was denied by a fine last-ditch challenge from Sandwith just after the hour mark, and then Danny Boshell drove a shot straight at keeper John Danby.
Keeper Barnes had to be on his toes to make a smart save from a long range effort from Sandwith 15 minutes from time, and Wilson shot narrowly wide as the game looked set to end in stalemate until the dreadful mix-up allowed Grimsby to take all three points.