Jean-Paul Kalala and Wayne Gray pounced to score inside five second-half minutes to secure a comfortable win.
With their place in the League One play-offs assured, Yeovil manager Russell Slade chose to rest a number of key players, including captain Tom Skiverton and the influential Chris Cohen, while handing a debut to youth team striker Tom Clarke.
The young forward would have fancied his chances against a side that has leaked over 70 goals this season, but he saw little of the ball in a first half dominated by defences.
With both sides restricted to long-range efforts, Steve Mildenhall was called upon to produce the only save of note, beating away Danny Spiller's thumping 25-yard drive in the 33rd minute.
Minutes later, Nicky Southall was next to try his luck, but his well-struck shot from the edge of the area was met by a fine block from Glovers centre-half Terrell Forbes.
But as the home side looked to push on in the second period, they were caught out by a rare Yeovil attack, falling behind to Kalala's strike in the 63rd minute.
Danny Jackman reacted well to intercept Gray's lay-off inside the area, but the ball fell to the unmarked Kalala who swept it past Simon Royce from 20 yards, just inside the post.
Five minutes later the Somerset outfit were celebrating again when Gray got on the end of Mark Lynch's throughball and calmly lifted the ball over Royce into the net.
Gillingham had chances to reduce the deficit, but both Danny Spiller and Mark Bentley failed to hit the target with headers from successive Clint Easton crosses.
Yeovil will now take on Nottingham Forest in the play-offs, with the first leg at Huish Park on Friday.