Harrow should have gone ahead on 18 minutes as Josh Webb cut inside before seeing his effort crash off the underside of the bar and away to safety for the Blues. The Gate had to wait until the 26th minute to force their first opportunity as Daniel Akindayini saw his effort rise over the bar.
That chance seemed to spur the Blues on as Adam Cash saw an effort fly wide before Chris Sessegnon turned provider for Elliott Buchanan who blasted his shot high over the bar.
The Gate’ fell behind on 38 minutes as a quick break away from Francis Babalola who ran unchallenged before popping a low shot past the outstretched hand of Bull to fire the visitors into a 1-0 lead at half-time.
Margate started the second half in a similar fashion to the first as they allowed Harrow to push for their second goal and they almost got it on 50 minutes Ibrahim Meite snuck through the back line and dragged his effort inches wide when through on goal.
The Blues grabbed an equaliser on 57 minutes after some fantastic work from Akindayini who chased the ball down before squaring to Buchanan who smashed the ball home via the post to restore hope for the Gate’.
That picked the Blues up as they began to attack the Harrow defence but they were caught out in the 67th minute as Lewis Driver, the scorer of Harrows equaliser on Saturday was left free to head home from 6 yards after Bull made a fine save from Meite.
That goal only helped spur the Ryman Premier League side on further and they should have been further ahead moments later as Bull made two fantastic saves from Meite to deny Harrow a more comfortable lead.
Defeat was confirmed in the 80th minute as Meite raced through the back-line before slotting past Bull to confirm Harrows place in the 1st Round Proper and an away trip to League One side Northampton Town.
MARGATE: Bull, Sessegnon (Mambo 78’), Tumwa, M.Johnson, Fitzsimons, Parry, Moore, Cash (Thalassitis 70’), Buchanan, Akindayini (Barrington 73’), Osborn
Subs not used: Foster