All the chances fell to Grimsby but they were not taken until, with five minutes to go, the vital moment came.
A free-kick on the left by Danny Boshell caught in the wind and keeper Ben Smith could only touch the ball onto the bar with Jones nodding in from a couple of yards out.
The afternoon went from bad to worse for Lincoln when they had skipper Scott Kerr sent off in the last minute for a second bookable offence.
At the end of the day, Lincoln had just the one goal scoring opportunity from a header by Lee Frecklington which went wide.
At the other end, Grimsby wasted quite a few openings, although a header from man-of-the-match Robert Atkinson was brilliantly saved by Smith in the first half.
It was the sort of game that had 0-0 written all over it until Jones, who has scored match winners against Mansfield and Brentford of late, made it a third with his vital touch.
The victory - only Grimsby's third at home this season - erased the memory of the Boxing Day defeat at home to Accrington, but this was Lincoln's third successive loss over the holiday period and real cause for concern for manager Peter Jackson, who had appeared to be turning things around.
Grimsby now face difficult looking away games at Chester and Chesterfield, while Lincoln must be looking for full points at home to Bury on New Year's Day.
With the early kick-off, Grimsby moved up four places in the League Two table, with Lincoln still right in the thick of the relegation dogfight.