Captain Adam Miller scored the only goal to give Gillingham their third straight win and put them above promotion rivals Exeter in the process.
The visitors almost broke the deadlock when Neil Saunders' shot deflected off Simon King and on to the crossbar.
Gillingham then hit the woodwork when when Nicky Southall's free-kick rattled the bar and bounced away to safety.
Miller had an effort ruled out for offside but was not to be denied as he later tapped in the winner.
Gillingham: Royce, Lewis, Bentley, King, Nutter, Southall (Peters 84), Weston, Miller, Barcham, Jackson (Cumbers 90), Oli. Subs Not Used: Richards, Julian, Steer.
Goals: Miller 79.
Exeter: Jones, Tully, Edwards, Seaborne, Archibald-Henville (Taylor 61), Moxey, Saunders (Harley 69), Gill, Obersteller (McAllister 46), Panther, Stansfield. Subs Not Used: Marriott, Basham.
Booked: Edwards, Stansfield, Moxey.
Att: 5,638
Ref: Graham Horwood (Bedfordshire).
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