Neil Saunders' late free-kick sealed victory for Exeter at St James' Park.
Marcus Stewart fired the Grecians into a half-time lead from Adam Stansfield's lay-off, but on-loan Jake Robinson levelled on his debut with a low shot.
Ben Harding smashed in from 20 yards to put Shots ahead but City were gifted an equaliser when Anthony Charles headed over his stranded keeper.
Saunders then curled in from 18 yards and keeper Paul Jones saved Harding's deflected shot to secure the win.
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