The teenage striker struck either side of half-time to make it three goals in his last two games and leave Alan Knill's side facing the drop.
Crystal Palace's victory over 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 hopes that Scunthorpe 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.
Michael O'Connor did pull a goal back four minutes from time after Darren Ward had fouled Joe Garner, but it was too little, too late and Millwall held on for a win that leaves them two points behind sixth-placed Nottingham Forest.
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.
But the Lions were in front seven minutes before half-time when James Henry teed up Marquis, who was left with the simple task of tucking home from a yard out.
The visitors were fortunate to be in front, but they could have been further ahead before half-time had Michael Nelson not produced a timely block to deny Henry.
But the Londoners did double their lead five minutes after the break after a mistake from Eddie Nolan.
The full-back headed straight to Marquis and the teenage striker made him pay with a first time strike from the edge of the area that gave Murphy no chance.
Scunthorpe boss Knill made a double substitution, with O'Connor and Bobby Grant replacing Nolan and Mark Duffy in a bid to salvage something from the game.
But a well-drilled Millwall side were looking increasingly comfortable, with the Glanford Park faithful stunned into silence.
Chris Dagnall and Grant both fired in long-range efforts but Forde was not troubled on either occasion.
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 precious points to make it a miserable afternoon for Scunthorpe.