Barry Hayles and Alan Dunne scored their first goals for Millwall to heap more pressure on Gillingham player-manager Andy Hessenthaler.
Hayles, in his first start since recovering from a cracked rib, latched on to Dunne's through ball to turn and fire home from 20 yards out ten minutes before half-time.
Then winger Dunne marked his return to the side from suspension just before the break when Jody Morris released him down the right flank to calmly slot in from 18 yards.
Adam Nowland gave the visitors hope two minutes after the break with a 25-yard wonder goal, after he was put through by Nicky Southall's short free-kick.
Nowland's goal sparked the visitors into life, and the West Ham loanee could have drawn Gillingham level on 50 minutes when they were awarded a free-kick just outside the area, but he blasted straight at the Millwall wall.
But Hessenthaler, who blazed Gillingham's best first-half chance over the bar, must now he is on borrowed time as they slumped to their sixth straight defeat.
The goals were just reward for Millwall's dominance over Gillingham, who last won on August 30 and could not muster a single shot on target throughout the first half.
Hessenthaler summed up his club's luck six minutes into the match when he ended one of their few attacking moves of the match by firing wildly over Millwall's bar from eight yards out, after Patrick Agyemang's good build-up work.
But Millwall defender Darren Ward had two opportunities in as many minutes to guide his manager Dennis Wise's free-kicks into the net, but deflected into the sidenetting before sending the ball harmlessly wide.
Jo Tessem should have done better with Millwall's first goalscoring chance - just three minutes into the match - when he robbed Nyron Nosworthy near the byline, only to shoot straight at goalkeeper Steve Banks.
Millwall keeper Graham Stack, on loan from Arsenal, was forced off with blood streaming from his face on 21 minutes, following a collision with Agyemang as he dived at the striker's feet.