Captain Danny Shittu headed home Chris Taylor's corner in the 42nd minute of the sixth-round replay at Ewood Park, and it proved enough to take the Lions - runners-up in 2004 - through to the last four on the weekend of 13/14 April.
As in Sunday's meeting at The Den at the weekend, Blackburn sorely lacked creativity and £11million strike force Jordan Rhodes and Leon Best drew a blank once more, although the latter had a second-half shot superbly cleared off the line by Shane Lowry.
Millwall now face a rematch of their 1999 Wembley defeat to Wigan in the Football League Trophy final, while results on Saturday could send Rovers into Sunday's east Lancashire derby against Burnley just three points above the relegation zone - an unthinkable second-consecutive relegation hovering ominously into view.
Blackburn started brightly and, having failed to register a shot on target at the weekend, they tested Lions goalkeeper David Forde through Best's speculative fourth-minute drive.
The Republic of Ireland international had a left-footed effort deflected behind in the 15th minute and, from the resulting corner, club stalwarts Morten Gamst Pedersen and David Dunn combined for the latter to arch a shoot past the far post from 18 yards.
Moments later, Millwall attacked and Danny N'Guessan felt he was impeded in the area by Rovers skipper Scott Dann when trying to reach Andy Keogh's cross, but referee Mark Clattenburg disagreed.
In the 20th minute, Blackburn goalkeeper Jake Kean created danger all of his own making by leaving himself stranded en route to claiming a long Lowry free-kick that Rob Hulse glanced wide.
N'Guessan twice had shots blocked by Jason Lowe as Rovers failed to clear a corner before Taylor's deflected shot crashed into the side netting.
The former Oldham midfielder delivered the next set-piece and Shittu was allowed room to power home from close range.
In the second half, Lowry produced a telling block when Josh King volleyed goalwards after Dann headed Pedersen's 49th-minute corner across goal.
Pedersen wasted a promising free-kick position as frustrations among the home faithful audibly grew, but Best brought them to their feet in the 63rd minute, drifting through a static Millwall backline to see the sliding Lowry clear his from the goalmouth.
However, Rovers' challenge faded badly. Mark Beevers blocked a Nuno Gomes strike in the final minute before Taylor blazed wastefully over when trying to add late gloss to the scoreline.