Kevin Ellison's second-half strike secured victory for Chester City.
Chester went ahead when when they made the most of an advantage when Richie Partridge crossed for John Murphy to head home unchallenged.
Grimsby equalised in stylish fashion when Peter Till crossed for Danny Boshell to head in from eight yards.
Ellison won it when he steered in a rebound off the post while the Mariners were unlucky to see Gary Jones head against the post as Chester held on.
Grimsby: Barnes, Mulligan (Whittle 74), Bennett, Fenton, Newey, Till, Clarke (Jones 53), Bolland, Boshell, Toner, Rankin (Taylor 64).
Subs Not Used: Montgomery, Bore.
Goals: Boshell 25.
Chester: Danby, Marples, Linwood, Butler, Wilson, Partridge, Grant (Sandwith 46), Hughes, Ellison, Murphy, Lowndes (Yeo 43).
Subs Not Used: Palethorpe, Rutherford, Carroll.
Goals: Murphy 10, Ellison 47.
Ref: Fred Graham (Essex).