They had a great chance to break their barren spell after 12 minutes as Jerson Dos Santos won a penalty, only to see Dean Morgan blaze it over the bar.
Although Margate dominated the first half, Gosport should have scored when Ben Wright somehow turned Nick Bignal’s shot onto the bar from a yard out.
A superb, sweeping move from the Blues saw Jeffrey Monakana square the ball for Dos Santos who could only poke a shot wide of the target on the slide.
Morgan nearly made amends for his penalty miss a minute into the second period but Nick Jordan superbly clawed away his acrobatic effort.
Ben Wright again went close for the visitors when he turned in the box and sent a shot just a foot over the bar.
Morgan then flashed a dangerous ball across the six yard box, just evading Jackson and free-kick inches wide of the target.
Ben Swift, a rock at the back in a man of the match performance for the Gate, then had Jordan at full stretch with powerful headers from consecutive corners.
When it looked like time was running out Jordan wiped out Pape Gueye, which saw him given his marching orders, to hand Margate their second penalty. Jackson kept his composure after a lengthy delay to score Margate’s first league goal in 943 minutes.
The wait for their next goal was a lot quicker as Jackson slotted home from close range from Gueye’s pass in injury time to record Margate’s first win in the league since October 8th.
Margate: Ward, Sessegnon, Palmer, Rogers, Moore-Azille, Swift, Monakana, Hamilton, Thalassitis (Gueye 71), Morgan (Fanimo 65), Dos Santos (Jackson 45). Subs not used: Akindayini, Adelakun.