Daniel Akindayini was then denied by former Blue Chris Lewington, who stuck out a big toe to divert the striker’s goalbound effort inches wide.
Welling struck late in the first half when Coombes sent Valerie Pajetat the wrong way from the spot after Christian Nanetti was tripped in the box by Tommy Cooney.
Substitute Nathan Fox flashed a couple of shots wide of the target early in the second half before Nanetti squandered a big chance when he sliced an effort over the bar from 10 yards.
However, his quick free-kick routine saw him shoot from the edge of the box, where a cruel deflection saw the ball nestle in the back of the net.
George Oakley headed agonisingly wide while Harry Crawford’s long range effort was tipped over the bar by Pajetat as the visitors smelt blood.
Pajetat pulled off a stunning save to deny Coombes late in the game, flinging himself to his left to beat away his fierce close range effort.
However, Coombes wasn’t going to be denied again when he twisted in the box and slotted high past Pajetat to seal the points.
Margate: Pajetat, Taylor, Cooney, Phipps, Moore-Azille, Johnson, Adelakun (Fanimo 65), Richefond, Akindayini, Banya (Fox 35), Henshall. Subs not used: Odofin, Williams, Foster.
Welling United: Lewington, Fish, Brown, Hatton (Dubois 88), Hayles, Francis, Nanetti (Walker 75), Waldron, Crawford (Fuseini 88), Coombes, Oakley. Subs not used: Johnson, Williams.
Margate Man of the Match: Valerie Pajetat