Two goals from John Marquis all but consigned Scunthorpe to League One and kept Millwall in the hunt for a play-off place.
The Lions went in front when Marquis tapped in James Henry's cross.
A mistake by Eddie Nolan set up Marquis's second, the full-back heading straight to the striker, who fired in from the edge of the area.
Michael O'Connor got a consolation goal for Scunthorpe from the penalty spot after Darren Ward fouled Joe Garner.
Crystal Palace's victory against Leeds leaves United six points behind the Eagles with a significantly inferior goal difference and just two matches remaining.
Just one defeat in four games had raised Scunthorpe hopes that they could avoid the drop, but Marquis, only leading the line in the absence of Steve Morison, Neil Harris and Kevin Lisbie, made almost certain that they will start next season in the third tier.
For Millwall, the win leaves them two points behind sixth-placed Nottingham Forest with two games to play.
The Iron made a positive start and Michael Collins fashioned a chance to open the scoring after nine minutes but the midfielder's curled effort from an acute angle flashed past the far post.
In-form midfielder Ramon Nunez tried his luck from long range but the Honduras international's drive flew over Lions goalkeeper David Forde's crossbar.
Scunthorpe remained on the front foot and left-back Marcus Williams burst into the penalty area but shot straight at Forde, who palmed the ball away.
Millwall started to get into their stride and the lively Andros Townsend let fly with a strike from 30 yards out, but Joe Murphy made the save.
Seven minutes before half-time, the Lions were in front. James Henry teed up Marquis, who was left with the simple task of tucking home from a yard out.
The visitors were fortunate, but they could have been further ahead before half-time had Michael Nelson not produced a timely block to deny Henry.
But the Londoners doubled their lead five minutes after the break after a mistake from Nolan.
The defender headed straight to Marquis and the striker made him pay with a first-time strike from the edge of the area that gave Joe Murphy no chance.
Scunthorpe were given hope four minutes from time when Ward brought down Garner and O'Connor tucked home the resulting spot-kick.
But Millwall were not troubled after that as they secured three vital points towards their push for the play-offs.