Millwall, having made three changes to the side that earned them their first win of the season against Oldham at the weekend with Richard Shaw, Derek McInnes and Marvin Williams making way for Zoumana Bakayogo, Samy Mawene and Chris Hackett respectively, had the better of a largely forgettable first half.
The 22-year-old Hackett impressed down the right wing and was instrumental in the home side's first real chance of the game on 20 minutes. He whipped a vicious ball across the box to pick out Tom Brighton at the far post, but Duncan Jupp put him under a lot pressure and the ball squirted clear.
The visitors rarely troubled Millwall, indeed it took 35 minutes for them to trouble Lenny Pidgeley in the Lions goal when Clint Easton hit an optimistic drive from 30 yards that bounced inches wide of the post.
The diving Pidgeley, of course, will say he had it covered all the way.
It was always going to take an error to break the deadlock, and five minutes before the break Brent Sancho obliged by losing his footing in side his own half and Kevin Braniff pounced, ran goalwards and slid the ball past the advancing Darren Randolph and into the bottom corner.
The two were involved again just after the break when Braniff made himself a yard of space with a clever chest control and turn, this time though Sancho snuffed out the danger with an excellent sliding tackle on the edge of his six-yard box.
Gillingham's best effort came from skipper Michael Flynn who had his powerful volley from the edge of the box tipped round the post on 70 minutes by Pidgeley after Millwall failed to clear Easton's corner.
The warning signs were there and they finally equalised with ten minutes left through second half sub Gary Mulligan on 81 minutes when he headed home Easton's corner from the same side.
The home side secured the win five minutes later when Hubertz headed home Brighton's corner.
Pidgeley came to the rescue in injury time when he saved well at the feet of Mulligan when he burst clear of the defence.