Hubertz volleyed home from close range with Rovers appealing in vain for offside after he latched on to a right-wing cross from Neil Harris seven minutes from time.
It was rough luck on Doncaster, who deserved at least a point, but the goal rounded off a hard-working display by the Lions, who had to come from behind.
The teams were level on points before the game but Rovers looked by far the better side at the start.
Paul Green had a shot deflected over the bar following a free-kick in the seventh minute and Doncaster went ahead six minutes later.
James Coppinger fired home a well-directed shot from an angle after Paul Heffernan and Danny Cadamarteri had both seen efforts blocked.
Heffernan was inches away from adding a second with a splendid curling shot in the 26th minute before Millwall began to get a foothold in the game.
The visitors worked hard throughout and were rewarded when Marvin Williams equalised in the 38th minute with a close-range volley after Hubertz had crossed from the left.
Coppinger had an angled drive parried and after beating two men just before the interval, but it was Millwall who looked the more threatening after the interval.
Hubertz fired home only to have the effort disallowed after brushing aside teenage defender Harry Worley in the 49th minute and Rovers suffered a blow when top-scorer Heffernan limped off soon afterwards.
Doncaster were denied a penalty when Tony Craig brought down Cadamarteri in the 61st minute, but worse was to follow for the home side.
Hubertz looked offside when he raced on to Harris's right-wing cross in the 83rd minute, but the flag stayed down and he volleyed home to the delight of the visiting fans.