Gate had taken seven points from a possible nine in previous three away games in Vanarama National League South but despite a grandstand finish they could not overcome the damage of conceding two goals in eight first-half minutes.
In the third meeting between the sides already this season, Kane Wills did pull back a goal Terry Brown's men probably deserved with 13 minutes remaining, but they could not find the second which would have extended their unbeaten away run.
Lewis Taylor (achilles), Jake Goodman (foot), Christian Jolley (ill) and Charlie Allen (suspended) didn't travel to Cornwall while Danny Green and Charlie Wassmer watched the whole game from the bench.
The early pressure all came from City and Gate keeper Nikki Bull got down well to stop a fierce drive from Cody Cooke from 18 yards inside two minutes.
Arran Pugh saw a header blocked from the resulting corner while at the other end Jamie Taylor curled wide of the far post on six minutes and Ryan Moss should have done better than sidefoot tamely at Tom McHale soon after.
There were more heroics from Bull diving to his left to tip out a scrambled Pugh effort from no more than six yards out, with Ollie Knowles lashing the rebound over the bar and towards the monstrous bonfire set to be lit later in the week.
Margate were more than holding their own but the breakthrough game on 23 minutes when the impressive Dan Green broke down the right and pulled back for the unmarked Cooke to side-foot inside the far post with Bull helpless.
The game looked all but up just eight minutes later when Margate's defence went to pieces after another good ball into the box from Green.
After pinball in the area the ball broke to Duff who's initial effort was blocked by Wilson, only for the striker to slide to prod past Bull at the second time of asking.
There were however furious appeals for a Gate penalty after Freddie Ladapo glided into the box after some neat passing from the visitors, however the frontman couldn't get the ball into position to shoot from 12 yards and his tumble under pressure looked just a bit late to convince referee Gary Parsons.
Margate looked the better side after the break but with very little in the way of action in the final third until the dying minutes.
Moss sent a shot straight at McHale after a neat turn and Nathan Green's prodded free-kick from 25 yards on 56 minutes was flapped aside at the second attempt by the keeper, but otherwise the game was played-out in the middle of the park.
At the other end Bull kept Gate hopes alive with a smothering save to deny sub Isaac Vassell who had been played through after some suspect defending while the tireless Ladapo enjoyed no success despite chasing umpteen balls down the channels and to the byline.
Wills gave the visitors hope with 13 minutes remaining when his angled drive from the right of the box found the far top corner, though Vassell jinked through from the restart and only Bull prevented it becoming 3-1.
Gate pressed forward in the closing stages and Wills again tested McHale from distance while Moss saw a 20-yard lob caught under the bar by the keeper but they could not find an equaliser before embarking on their longest return journey of the season.
Truro: McHale, Mitchell, White, Ash (Afful 67mins), Richards, Pugh, Knowles, Green, Duff (Vassell 61mins), Reid, Cooke (73mins Barrow). Subs not used: Wright.
Margate: Bull, Rents, N Green, Hunt, Wilson, Johnson, Wills, Moore, Ladapo, Moss, J Taylor (Taiwo 67mins). Subs not used: Wassmer, D Green, Cash, Stewart.