Clint Easton and Matthew Jarvis scored a goal in either half as Millwall's awayday blues continued.
The Lions have now failed to reap any return from their four League One matches on their travels this season - but it wasn't for the want of trying at Priestfield.
At times Nigel Spackman's side produced some periods of possession, but it was a frustratingly similar scenario with a lack of penetration in the final third.
Millwall boss Spackman handed a trio of players their full League debuts with Ali Fuseini, Zoom Bakayogo and Chris Zebroski included in a starting line-up that also saw Alan Dunne make his first League start of the season.
But The Lions had barely time to get into their stride before Gillingham had taken the lead courtesy of a wonder-goal from Easton, who let fly with a 30-yard screamer.
However, The Gills could count themselves a tad fortunate that seconds before that they were not penalised when Dunne was clearly obstructed as he tried to sprint clear. The ball fell to Easton, and his strike would have beaten any keeper in the country.
Millwall went agonisingly close to levelling within 60 seconds, but Zak Whitbread's header from a Dunne corner flashed a yard wide of the mark.
From then on it was virtually one-way traffic in the opening half as The Lions started to exert pressure on the Gillingham defence.
Fuseini showed great technique and quick-thinking when he reacted first after another Dunne corner was hacked clear, but saw his stinging volley sizzle just off target.
Home keeper Scott Flinders blocked at the near post from Bakayogo, and then a lovely backheel by Byfield found Bakayogo, but his low delivery was held comfortably by Flinders.
Millwall introduced Maurice Ross for Whitbread a couple of minutes into the second half and again it was The Lions who pressed forward with the impressive Fuseini spraying the ball around with a maturity that belied his tender age of just 17.
Twice the teenager found Bakayogo on the overlap, but twice the Frenchman's delivery was unable to reflect the quality of Fuseini's initial pass.
But just when The Lions looked as if they were going to push on and get something for their efforts, Gillingham effectively killed the game with a second goal on 63 minutes.
Again, there was a slightly fortuitous decision that went the home side's way - this time when Byfield was the meat in a defensive sandwich, but referee Ray Olivier ignored his appeal for a foul.
Within seconds the ball was at the other end of the field and in the back of the net, courtesy of a smart angled finish by Jarvis on the right.
Spackman responded by bringing on Marvin Williams and then Poul Hubertz for Bakayogo and Zebroski, but it was the home side who could have added a third on 74 minutes when Jarvis fired over with the goal begging after good work from Jarvis.
Millwall refused to give up though, and should have reduced the arrears seven minutes from time when Hubertz chested Richard Shaw's long ball into the path of the onrushing Dunne, but the midfielder screwed his shot wide.
The Lions handed themselves a lifeline with three minutes remaining courtesy of Hubertz's flicked header from a Williams centre - his third goal of the season.
And the visitors were inches away from grabbing an injury-time equaliser when Ross floated in a free-kick, but the ball curled excruciatingly away from the unmarked Paul Robinson at the far post.
To sum up Millwall's luck on the night, Elliott launched a long ball into the danger zone in the dying seconds and Dunne flicked on perfectly into space for Byfield. At any other moment previously the striker would have been free to run onto the ball and have a clear shot at goal. Unfortunately, Byfield had fallen to the ground a split-second earlier suffering with cramp.

Gillingham: Flinders, Jupp, Flynn, Cox, Crofts, Bentley, Mulligan (Spiller, 85mins), Easton, Ndumbu Nsungu (McDonald, 78mins), Jarvis, Johnson. Subs not used: Pouton, Clohessy, Stone.
Bookings: Flinders (22mins), Bentley (45mins)
Scorers: Easton (13mins), Jarvis (63mins)

Millwall: Day, Senda, Robinson, Shaw, Whitbread (Ross, 49mins), Bakayogo (Williams 68mins), Elliott, Fuseini, Dunne, Zebroski (Hubertz 71mins), Byfield. Subs not used: Pidgeley, Ardley.
Bookings: 22 Byfield (22mins), Zebroski (35mins), Shaw (56mins)

Ref: Ray Olivier
Attendance: 7,134