Alex Jeannin gave the Grecians the lead at the start of the second half direct from a corner kick.
Lee Phillips stretched the scoring with a lob over the goalkeeper and veteran striker Steve Flack wrapped up the scoring with a close-range strike.
Gravesend survived an early penalty scare when goalkeeper James Pullen appeared to pull down City striker Flack inside the box but the referee waved away appeals from a host of City players.
Gravesend offered little as an attacking force early on and seemed happy to sit back and soak up the pressure. They didn't muster a single attempt on goal in the first 45 minutes.
Exeter enjoyed plenty of possession but lacked the cutting edge in the final third.
Flack headed over the bar from Scott Hiley's cross as Exeter pushed forward and Pullen made a superb double save from Paul Buckle then Flack as Gravesend held on.
In the closing stages of the first half Gareth Sheldon fired over the bar after meeting Flack's flick at the far post.
Exeter took the lead just two minutes after the restart. Jeannin whipped in a wicked curling free-kick which flew past everyone and drifted straight into the top corner.
Four minutes later Sheldon picked out Phillips and he lobbed the ball over the advancing goalkeeper.
It took Gravesend an hour to create their first attempt on goal, Jean-Michael Sigere heading Andy Drury's cross tamely past the post.
Sheldon had a shot scrambled off the line by Lee Gledhill and Phillips headed just wide as Exeter dominated.
With 10 minutes left Flack sealed it for the Grecians when he bundled home Jeannin's corner at the near post.