It wasn't pretty but the young Lions earned all three points over their London rivals in a wet and wild Professional Development League derby on Monday afternoon.
Noel Leighton stepped off the bench to complete a fine fightback as Kevin Nugent's men came to life in the second-half after finding themselves a goal down at the break.
QPR seemed to be in control and cruising until the 72nd minute, when Millwall forward Kris Twardek fired home the equaliser after some sustained pressure.
At 1-1 the match descended into a scrap as both sides pressed for a late winner in the intermittent rain.
But it would be the hosts who would secure the bragging rights as forward Noel Leighton capped off a good counter-attacking display with a goal eight minutes from time.
The fixture was also an opportunity for first-team players Tony Craig, Ben Thompson and Shaun Williams to get valuable match minutes under their belt.
Midfielder Shaun Williams, who came off the bench in Millwall's draw at Aston Villa on Saturday, played 60 minutes for the young Lions as he continues his rehabilitation on a injured knee.
Millwall: King, McNamara, Craig (Mitchell 70'), Thompson, Mbulu, Rooney, Donovan, Williams (Skeffington 60'), Brymora (Leighton 47'), Twardek, Chesmain. Subs not used: Girling, Topalloj.