Danny North found the target twice to give Grimsby a third straight away victory and end Chesterfield's winning streak at four games.
North spun past Aaron Downes to score the opener in first-half injury time after crowd trouble had seen 10 fans ejected from the ground.
North's second came from the penalty spot after he and Downes had collided in the area on 78 minutes.
Jamie Ward pulled a goal back for Chesterfield with seven minutes left.
Chesterfield: Roach, Lowry, Kovacs, Downes (Allison 90), Robertson, Rooney, Niven, Winter (Barnes 59), Leven, Ward, Fletcher.
Subs Not Used: Jordan, Davies, O'Hare.
Booked: Downes.
Goals: Ward 83.
Grimsby: Barnes, Hird, Bennett (Fenton 66), Newey, Atkinson, Hegarty, Hunt, Clarke, Bolland, North, Jones.
Subs Not Used: Montgomery, Till, Taylor, Butler.
Booked: Bennett, Newey.
Goals: North 45, 78 pen.
Att: 4,540
Ref: Eddie Ilderton (Tyne & Wear).