Charlie Cooper's free-kick and Corey O'Keeffe's header had given Blues a deserved lead inside 25 minutes before Harry Smith pulled one back for the visitors before half-time.
Richard Beale's side stood firm to Millwall's direct style and looked to have sealed the win, before Rooney's late header from an out-swinging corner secured Millwall a point.
Blues started the half on the front foot and dominated large parts of the early proceedings.
A neat David Popa flick continued a bright Blues move and Cooper just couldn’t make a clear contact on O’Keeffe’s cleared cross.
Millwall, who hadn't settled into the contest could have took a surprising lead.
Rooney rised high and Cooper, who was at the far post, read the situation perfectly and cleared off the line.
Blues continued to press and finally got their rewards after 14 minutes. Popa was fouled, just outside the penalty area, and from a central position, Cooper thrashed a free-kick through a crowd of bodies and past Tom King.
And with Blues dominating it became 2-0 nine minutes later. O’Keeffe peeled away at the far post and headed Steve Seddon’s cross into the far top corner.
It was what Blues deserved, but Millwall responded.
Smith, who was in the middle of a crowd of bodies, rose high at the near post and headed an inswinging corner past Trueman.
The visitors sensed an opportunity and Trueman did excellently to keep Blues in front as he got low and tipped Brown’s sidefooted effort round his near post.
Half-time - Blues Under-23s 2 Millwall Under-23s 1
Blues started the half like the first and could have taken the lead five minutes in.
Popa’s excellent control created a pocket of space and he found McDonald inside, but his effort was deflected into the near post sidenetting.
Buoyed by their pressure, Blues continued their domination and could have extended their lead further.
Viv Solomon-Otabor reached the left byline and found Popa with a good cross, but the striker’s near post header was excellently saved one-handed by a full stretched King.
It was a terrific save from the ‘keeper and Millwall nearly equalised minutes later.
King was left unmarked, 12 yards out, but instead of finding the empty corner he diverted his right-footed effort wide of the far post.
Both sides continued to battle in midfield, but neither side created anything substantial.
Blue however had looked to have rode a decent spell of late Millwall pressure, but they were undone by another corner.
A right wing delivery was curled to the far post and Rooney’s header looped into the vacant far corner.
The visitors sensed victory and deep into stoppage time Kris Twardek forced Trueman into an excellent save low save.
Blues Under-23s: Connal Trueman, Josh Cogley (C), Steve Seddon, Luke Maxwell, Noe Baba, Josh Martin, Corey O’Keeffe, Charlie Cooper, David Popa, George O’Neill (Wes McDonald 45+1), Viv Solomon-Otabor
Subs not used: Jake Weaver, Beryly Lubala, Edji Mbunga, George Taylor.
Goals: Cooper 14, O'Keeffe 23
Millwall Under-23s: Tom King, Shaun Cummings, Noah Chesmain, Harry Donovan, Rian Bray, Paul Rooney (C), James Brown (Kyron Mundle-Smith 75), Kyron Farrell, Harry Smith, Jamie Philpot, Kris Twardek
Subs not used: Ryan Sandford, Dan McNamara, Lewis White, Eze Ebuzoeme,
Goals: Smith 35, Rooney 88