Brennan Dickenson put Gills ahead before Simon Gillett equalised but Aaron Morris quickly restored the visitors' lead, before Glovers defender Seth Nana Ofori-Twumasi was sent off shortly afterwards.
The early exchanges echoed the previous weekend's performances as both sides felt their way into the game.
Gillingham were gifted an opener after 23 minutes courtesy of a mix-up at the back. Former Exeter goalkeeper Artur Krysiak came racing out to meet a through ball, only to stumble into covering defender Aaron Martin.
Gills striker Dickenson refused to give up on the opportunity and nipped in to poke into the gaping net, leaving the Yeovil pair in a heap on the floor.
The Glovers had opportunities to level in the first half - first through former Chelsea man Ofori-Twumasi, who stung the palms of Glenn Morris before Kieffer Moore's strike was cleverly turned round the post by the Gills stopper.
The new-look Huish Park outfit grew into the game but lacked any penetration in the final third.
They could have fallen further behind five minutes before the break when skipper Doug Loft's fizzing left-foot strike from distance was parried by Krysiak but no-one from the away side was able to follow up.
Yeovil improved in the second half and began to fashion one or two chances to give the sparse turnout cause for cheer.
They made the pressure count after 56 minutes with a well-worked set-piece as Joe Edwards rolled the ball to former Nottingham Forest man Simon Gillett, who unleashed a ferocious strike past Morris into the top left-hand corner of the net.
Gillingham were back in front just four minutes later though as the Glovers' back line allowed Aaron Morris all the time and space in the world to control, take a touch and pick his spot with a fine strike to the far post.
Yeovil's misery was compounded just after the hour mark when Ofori-Twumasi was shown a straight red for a late challenge on Luke Norris.
The south Somerset side refused to go out with a whimper though and created chances through Edwards and Nathan Smith.
In the end, it was the side with the stronger defensive performance that proved triumphant as the Gills won for only the second time in 10 matches against the team they face again in four days time in the league.