Several dangerous balls were flashed into the box as Margate dominated down the wings, with Orlando Smith especially lively.
He saw a shot fly over the bar, while Liam Friend also nodded a chance off target in a half of few chances.
However, just before the hour mark Smith broke the deadlock, capping a fine display, when he dropped inside from his right wing and shot low into the net, at the second time of asking.
Top scorer Frannie Collin then saw a 25 yard free-kick easily held by Melvin Minter as Margate pushed to add to their advantage.
Former Margate player Charles Banya should have had his side level soon after though, only to flash a shot wide when well placed in the box.
Substitute Henry Ikeije shot straight at Minter when set through on goal, while, breaking from that chance, Kurtis Cumberbatch saw an effort deflected just wide.
Cumberbatch then squandered an even better chance when his diving header flashed inches wide of the post from close range.
Just as it looked like Margate would take their winning run to seven games, Adam Richards picked up possession midway through Margate’s half and drove towards goal before firing a shot past Lenny Pidgeley into the bottom corner.
MARGATE: Pidgeley, Sessegnon, Mills, Rogers, Friend, Wynter, Smith (Bodkin 82), Prescott, May (Ikeije 32), Collin, Martin (Swift 82). Subs not used: Brown, Stannard.
HARROW BOROUGH: Minter, Moore, Uade, Richards, Ujah, Preddie, Banya, McLeod (Paquette 77), Stanislaus, Bryan, O'Connor (Cumberbatch 68). Subs not used: Cain, Davis-Coker, Hall.
Man of the Match: Tom Wynter