On-loan defender Mark Rogers headed home an 84th minute winner to earn Stevenage Borough the points, which maintained their chase for a play-off spot spot.
The game featured three penalties - all converted - before Rogers, on a month's stay from Wycombe Wanderers, pounced to get the vital touch on James Gould's corner and inflict Gravesend's first Conference defeat of 2004.
However, the match turned on a controversial incident after only seven minutes. Stevenage's Tunisian striker Dino Maamria went in heavily on Gravesend goalkeeper Alex O'Reilly.
However referee Woolmer decided to show a yellow card rather than red and Maamria stayed on to play an influential part in proceedings.
Graham Westley's side started well but fell behind after 19 minutes to the first of the game's spot kicks. Andrew Drury was brought down by Simon Travis and the home midfielder stepped up to beat Lionel Perez.
Then Maamria was adjudged to have been brought down under a challenge from Chris Moore, with the Kettering official again pointed to the spot and Maamria sent O'Reilly the wrong way to put Boro level.
Boro's second goal just after the hour was a carbon copy of the first. The Fleet defenders allowed him too much space and time, and again he went down with Mr Woolmer again deciding it was a penalty.
The execution was exactly the same with O'Reilly again guessing the wrong way.
Five minutes later, there were further problems for Gravesend. Justin Richards, a lively performer alongside Maamria, was hauled back by Francis Duku, and the hard-pressed referee brandished the red card, following a word with an assistant.
However, despite being a man short, Gravesend pulled level when Moore found himself free to score from close range, and it looked as though Andy Ford's part-timers were about to extend their hitherto undefeated record since the turn of the year.
Boro had other ideas though and having won two quick corners, the second created problems again at the back and Rogers rose above his marker to steer the ball past O'Reilly.
The match featured a total of seven yellows and one red, to add to the six yellows and a red handed out when these two teams met at Broadhall Way four months ago.
Stevenage are looking to be more consistent in the closing stages of the season but will have to keep winning in order to reach the play-offs, having been 5-1 joint second favourites to win it outright at the start of the season.