Two second-half goals were enough to give the Mariners the points in a match that failed to spark into life despite Chester boss Bobby Williamson ringing the changes after two defeats on the road over the festive period which had seen his side slip out of the play-off frame.
The home side had a good opportunity on 28 minutes when an overlap by Kevin Ellison created space on the left flank and his cross to the unmarked Richie Partridge was palmed away by keeper Phil Barnes.
A minute later Ellison broke through again and had a great shooting chance but skewed his effort well wide of the target.
The visitors produced a rare moment of threat five minutes from the interval when Robert Atkinson rose highest in the box to send a header looping narrowly over the bar.
Chester then wasted a golden chance on 42 minutes when a mix-up between Tom Newey and Sam Hird gave possession to Paul McManus who carried the ball 40 yards towards goal only to fire wide with just the keeper to beat.
Grimsby should have taken the led on 58 minutes when a cross from the right flank found the unmarked Danny Boshell who inexplicably headed over with the goal at his mercy.
Boshell did not have long to wait for a chance to redeem himself when his side were awarded a penalty after keeper John Danby brought down substitute Danny North in the 64th minute.
Boshell superbly dispatched the spot-kick which gave Danby no chance despite the keeper going the right way.
Simon Yeo headed over a sharp chance and then forced Phil Barnes into a smart save with a shot from the edge of the box as Chester pushed for a leveller.
But it was Grimsby who made the game safe as Paul Atkinson steered a glancing header inside the post from Newey's free kick seven minutes from time.