Tony McMahon, Scott McDonald and Leroy Lita were all on target as Boro displayed commendable spirit to overhaul a half-time deficit and secure just a fourth away win of the season.
The Teessiders refused to be cowed by a hostile home crowd, with the game twice having to be stopped in the second half because of missiles hurled from the stand.
Despite only joining on loan from Stoke City on Friday, Stockton-born Andrew Davies was thrust straight into the heart of a new-look Boro back five.
The remodel was no doubt a response to last weekend's second-half capitulation against Swansea City, but it was at the other end of the pitch where Boro, and Lita in particular, were found wanting early on.
Lita had two glorious opportunities in the opening seven minutes, but failed to find the target with either, directing a free header well wide of the target from a McMahon cross and prodding the ball wastefully into touch as he attempted to round Millwall goalkeeper David Forde.
As a result, the hosts were able to claim the lead in the 15th minute. They had already hit the crossbar at that stage, through a curling effort from James Henry, and their goal was as easy as they come.
Forde launched a long clearance downfield, Steve Morison won the flick on, and Neil Harris stole behind the Boro defence to volley past Jason Steele from close range.
Morison came close to adding a second with a half-volley that sailed over the crossbar shortly after the half-hour mark, before Lita wasted yet another glaring opportunity for the visitors.
Released by Julio Arca, the striker at least managed to get a shot away after rounding Forde, but he took the ball far too wide and a backtracking Paul Robinson was able to make a routine clearance from his own goalmouth.
The second half started with Millwall on top, but from nowhere, McMahon fashioned a sensational equaliser in the 58th minute.
Darren Purse conceded a free-kick against McDonald, and McMahon curled a superb 25-yard effort into the top left-hand corner of the net.
The equaliser came somewhat out of the blue, but four minutes later, and Boro ahead. The goal owed much to an instant impact from substitute Merouane Zemmama, who twisted past two defenders on the edge of the area.
The Moroccan slipped a deft through ball to McDonald, and the former Celtic striker drilled a low finish past Forde. The turnaround drew an angry response from Millwall supporters, and the game was twice stopped by the referee as missiles were thrown onto the field. The first was aimed at a linesman, but the second came close to hitting Boro goalkeeper Steele.
Play eventually resumed, however, and Millwall drew level with a set-piece special of their own with 12 minutes left.
Davies committed a foul around 28 yards out, and former Fuilham and Watford midfield Hameur Bouazza drilled a fantastic strike into the top left-hand corner.
Back came Boro again though, and the visitors reclaimed their lead with seven minutes left.
Zemmama was the instigator once again, picking the ball up on the right-hand side and delivering a teasing cross into the box, and Lita stole ahead of his marker to glance home a header from eight yards.
MILLWALL (4-4-2): Forde; Dunne, P Robinson, Purse, Barron; Henry, Trotter, Abdou, Hackett (Bouazza 65); Morison, Harris (Lisbie 76).
Subs (not used): Mildenhall (gk), Eastmond, Craig, Ward, T Robinson.
MIDDLESBROUGH (5-3-2): Steele; McMahon, Hines, Davies, Grounds, Bennett; Bailey, Arca (Zemmama 57), Taylor; Lita, McDonald (Smallwood 90).
Subs (not used): Ripley (gk), Haas, Park, Halliday, Boyd.
Source: Northern Echo
Source: Northern Echo