It could have been worse for the Mariners as Chester twice hit the woodwork in added time.
But the scoreline was cruel on the home side, who were pounding the Chester goal in the second half and it took two remarkable saves from John Danby to keep them in it at 1-1.
But when Grimsby were not awarded a free-kick, the visitors got one seconds later and Ellison scored a brilliant goal from the 25-yard set-piece.
Then four minutes from time, Ellison completed his hat-trick with a superb hook shot from 18 yards.
Grimsby had the chance to make the scoreline respectable when they were awarded a penalty just before the end.
But the afternoon was summed up when midfielder Danny Boshell struck his spot-kick wide of the post.
Chester had started the game brightly and Ellison out-paced Grimsby skipper Matt Heywood to go through and roll the ball past keeper Phil Barnes.
Grimsby altered their formation replacing Nick Hegarty with Simon Heslop on 28 minutes, but it was another substitute, Danny North, who came on and put Grimsby level.
Only three minutes of the second period had gone when Boshell's corner was headed goalwards by James Hunt and North turned the ball in from close range.
Then the decisive period came with Danby's superb stops from Nathan Jarman and Boshell as Chester survived a rocky period.
But the visitors rode their luck and they had their ace in the pack in the veteran Ellison, who once interested Grimsby.
But perhaps the result wasn't surprising as it was Chester's third successive victory at Blundell Park.