In a flurry of late drama, Crewe left-back Darren Moss scored against the run of play to put the visitors ahead six minutes from time, before super-sub Hubertz forced home an injury-time equaliser to extend Millwall's unbeaten run to four games.
A nip-and-tuck encounter had earlier seen Crewe open the scoring through Michael Higdon, before Millwall struck back on the brink of half-time as Darren Byfield headed home the 14th goal of an increasingly impressive season.
A second-half surge from Millwall should have seen them put the outcome beyond doubt long before Moss' intervention but, despite the outstanding efforts of attacking livewire Byfield, Willie Donachie's men could not break down a stubborn Crewe defence.
Crewe made the long trip south determined to make amends for the frustrating weekend loss to Gillingham, but the early signs were not auspicious for the visitors.
Just as at the Priestfield where Gradi's men dominated for long spells only to be undone by a lack of cutting edge in the final third, Crewe seemed to be in profligate mood with Higdon and Lowe missing decent early chances.
But when visiting goalkeeper Ben Williams made an instinctive goalline save from a close-range Marvin Elliott effort, Crewe launched an incisive counter-attack to open the scoring.
Squirming free of the combined attentions of Richard Shaw and Tony Craig on the right flank, Rodney Jack found the forehead of Higdon with a cross of inch-perfect precision, leaving the 23-year-old with the simple task of guiding an angled header across Lenny Pidgeley for his third goal of the season.
Millwall responded with an attacking flurry that yielded an equaliser on the stroke of half-time and Byfield nodded in from a precise Neil Harris centre.
With parity restored, the Lions re-entered the Den brimming with attacking verve.
But when Higdon flicked on a Lowe corner for left-back Moss to fire home at the back post, all Millwall's enterprise seemed to have come to nothing.
Cue the intervention of the 6ft 4in Hubertz, who fired home a cross from fellow substitute Chris Hackett to give Millwall a deserved share of the spoils.