Michael Reddy was a constant thorn in the side of the Chester back line, and he capitalised on a defensive slip to earn his side three points and end City's unbeaten start to the season.
An uneventful opening 20 minutes saw little of note aside from a badly miscued shot from visiting captain Justin Whittle, who had worked himself a good shooting opportunity.
The home side created an excellent chance on 21 minutes when Ryan Lowe carved open the Grimsby defence to send in Michael Branch, who shot wide.
Moments later another good move left Ben Davies with a good opening, but his goal bound effort was charged down by John McDermott.
Branch missed his kick as he sized up a volley after good work involving Davies, and Lowe flashed a header wide as Chester enjoyed the majority of possession.
The second period again saw the home side on the offensive and Lowe hit a shot on the turn, which was saved by Steve Mildenhall.
Five minutes after the interval Grimsby took the lead against the run of play after Phil Bolland needlessly pulled down Rob Jones for a penalty.
Jean-Paul Kalala Kamudimba stepped up to send Chris MacKenzie the wrong way from the resultant spot-kick.
It took Chester only three minutes to restore parity when Gary Croft's attempted clearance was charged down by Branch and Blundell centred to Lowe to fire home from close range.
Lowe then made a hash of another decent opportunity, shooting straight at Mildenhall when clean through on goal, and at the other end, Andy Parkinson inexplicably shot wide with only the keeper to beat.
Mildenhall came to the rescue of his side 20 minutes from time as he blocked a close-range effort from Lowe who had been picked out by an intelligent pass from Stewart Drummond.
Chester were made to pay for the missed opportunities when, 10 minutes from the end, Reddy took advantage after a slip on the halfway line by Luke Dimech and raced through on goal to slot past MacKenzie for the winner.