Lions skipper Paul Robinson rescued a point for his side with a vital equaliser with Millwall's first goal at The New Den since February 23.
Millwall started brightly with Croatian midfielder Ahmet Brkovic involved in everything and were almost in front after just nine minutes when Mark Bentley headed his cross dangerously close to Derek Stillie's right-hand post.
A minute later Brkovic then curled a 20-yard effort just wide, before attempting a cheeky lob from 30 yards that a back-peddling Stillie had to palm away.Nicky Southall's free-kick was Gillingham's first shot on target, but came in controversial circumstances when Lions defender Marc Laird caught Barry Fuller as he skipped past him in the inside left channel.
The contact was minimal and Fuller stayed on his feet while his assailant went to ground.
Well-placed to shoot and with Dennis Oli and Simeon Jackson square and in space, Fuller was enraged when referee Steve Bratt unnecessarily blew for the free-kick with the advantage so clear.
But the jeers from the 1,300 Gills fans in the North Stand behind the goal quickly turned to elation as Southall curled the ball superbly into Rhys Evans' top corner of the net.
Millwall's swagger evaporated instantly and only Danny Senda's low shot threatened the Gills goal in first-half stoppage time, but Stillie was equal to it.
The home side started the second period with more purpose, but then Brkovic somehow headed Senda's right-wing cross wide from six yards with the goal at his mercy when he found himself totally unmarked.
But it was the Lions captain Robinson who finally dragged his side back into the game when he fired in from the edge of the area after being teed up by sub Jay Simpson on 75 minutes.
Laird almost snatched all three points when he headed over late on after Stillie parried away David Martin's cross.