Mark Clattenburg was at the centre of controversy at Ewood Park as Danny ShittuÔÇÖs first-half header secured MillwallÔÇÖs place in next monthÔÇÖs FA Cup semi-final against Wigan Athletic at Wembley.
Kenny JackettÔÇÖs Championship outfit, who were beaten by Manchester United in the 2004 FA Cup final in Cardiff, overcame Blackburn in this quarter-final replay thanks to ShittuÔÇÖs goal following SundayÔÇÖs goalless draw at the New Den.
But Fifa official ClattenburgÔÇÖs decision to award a corner prior to ShittuÔÇÖs goal prompted anger among the Blackburn players, with the ball clearly going out for a goal-kick rather than a Millwall corner.
While SundayÔÇÖs first game at the New Den was a tense and fractious affair, there were at least some instances of goalmouth action to keep the crowd entertained, most notably ShittuÔÇÖs long-range efforts on the Blackburn goal.
But this fixture took an age to come to life, perhaps partly due to the vast banks of empty seats inside Ewood Park which contributed to the kind of atmosphere more in keeping with a reserve team game.
Without the injured midfielder David Bentley, back at Blackburn following a loan move from Tottenham, the home side lacked the creativity required to take charge of the game and they were restricted to half chances in the first half.
Aside from a David Dunn effort from the edge of the penalty area and a 20-yard shot from Josh King which flew 12 inches over the crossbar, Millwall goalkeeper David Forde was untroubled.
Millwall were equally unambitious, however, and they had to rely on ClattenburgÔÇÖs mistake for the chance which led to the opening goal on 42 minutes ÔÇö the first that Blackburn have conceded in this seasonÔÇÖs competition.
With Dany NÔÇÖGuessan appealing for handball after his shot had been blocked by the left arm of Blackburn full-back Jason Lowe, Clattenburg was distracted at the key moment as Chris TaylorÔÇÖs shot flew into the side netting.
There was no contact from any Blackburn defender as the ball whistled out of touch, but Clattenburg awarded a corner and ShittuÔÇÖs diving header from TaylorÔÇÖs delivery put Millwall ahead.
Clattenburg was then forced to step in as Taylor bickered with BlackburnÔÇÖs angry players on the way back to the centre circle, but if Michael AppletonÔÇÖs players had been fired up by a sense of injustice, it barely showed in their second-half performance.
Despite the arrival of Nuno Gomes, the home side had to wait until the 64th minute before they created a chance of note, but it required a goal-line clearance by Shane Lowry to deny Leon Best an equaliser.
Best had escaped the attentions of Taylor on the edge of the penalty area and drove towards the six-yard box before shooting goalwards, but LowryÔÇÖs intervention preserved MillwallÔÇÖs lead and increased the frustrations of the sparse crowd, which was 100 fewer than the 8,735 who saw Chesterfield defeat Wrexham at this stage of the Cup in March 1997.
Blackburn failed to create further chances to equalise and they almost conceded a second in stoppage-time when Taylor was released inside the penalty area.
But with only goalkeeper Jake Kean to beat, the midfielder scuffed his shot high over the crossbar.
Blackburn Rovers (4-4-2): Kean; Lowe, Dann, Hanley, Markus Olsson (Gomes h-t); King (Forrester 75), Dunn, Pedersen, Martin Olsson; Best, Rhodes.
Subs: Sandomierski (g), Givet, Rekik, Goodwillie, OÔÇÖSullivan.
Millwall (4-1-4-1): Forde; Dunne, Shittu, Beevers, Lowry; J Smith; Keogh, Trotter, Taylor, NÔÇÖGuessan (Abdou 66); Hulse (Marquis 85).
Subs: Taylor (g), Tyson, A Smith, Osborne, Saville.
Booked: Shittu, Beevers, Keogh.
Referee: M Clattenburg (Tyne & Wear).