The first half was scrappy but burst into life when Lee Phillips and Jamie Stuart were both sent off as the players left the pitch.
They squared up and appeared to clash heads leaving the referee with little option but to show red.
The second half was a much more open game and there were chances at both ends. Grays took the lead through John Martin but Exeter pulled level through a late Jon Challinor strike.
The Grecians looked set to come away with a point but in injury time Hooper stabbed home the winner for Grays.
It was a cruel end to the game for City in front of a bumper crowd of 6,682 at St James Park.
Grays started brightly and looked a threat in the opening stages. Michael Kightly had the first shot of the game when he fired wide from 20 yards in the third minute.
The Grecians created few opportunities in the first half.
Grays came close to finding an opener just before the break. Jamie Slabber ran powerfully to the edge of the box and when his shot was well saved by Paul Jones, Kightly thumped the rebound high over the bar.
The visitors eventually opened the scoring 10 minutes into the second half.
Dennis Oli picked out Martin who struck a fine shot past Paul Jones from 12 yards.
City pushed forward and hit the woodwork twice in quick succession.
Defender Billy Jones curled a free kick from 25 yards against the post before captain Glenn Cronin side-footed against the woodwork from 15 yards.
Exeter finally pulled level with three minutes left on the clock. Tony Scully's corner was flicked on by Gary Sawyer and Challinor fired home from close range.
Just when it looked like the points would be shared Grays snatched the winner in injury time. Stuart Thurgood's free-kick found Martin and his cross was steered home at close range by Hooper.