A Danny Shittu header put Millwall into an FA Cup semi-final against Wigan Athletic at Wembley in what will also double as a play-off for next season's Europa League. That is unless Chelsea finish outside the top five, though as they are seven points ahead of sixth-placed Liverpool this appears unlikely.

Kenny Jackett, the Millwall manager, said: "We'll start planning straight away. It's a big achievement to get there but we want to go there and do well. We want to go there and win. That's what Wembley is all about – it's about winners."

Played before a paltry 8,635 crowd – the lowest of recent memory for a quarter-final – this replay was scoreless until the 42nd-minute mark, when Shittu finished a Chris Taylor corner, meaning the teams had played for more than two hours (132 minutes to be precise) with no goals after the first match ended nil-nil.

The "closest" either team came to scoring before this came when a Leon Best shot went straight into David Forde's hands and a David Dunne curled effort went past the Millwall goalkeeper's right post.

Before what was Shittu's second of the season Dany N'Guessan had what looked a credible claim for a penalty for handball turned down by referee Mark Clattenburg after his shot hit Jason Lowe.

The corner Taylor won just before Millwall scored looked doubtful – whether there was a deflection from a Rovers player was moot – but when the former floated the kick in, Shittu scored with a thumping header. Of the corner, Jackett added: "We've had plenty of decisions go against us, it may have been a crucial one but it was a great header by Danny."

The second half featured Millwall playing for passages in the Rovers half, which was rarely the case before the break. Still, the sense was that Michael Appleton's Blackburn side might have the edge.

Best had Rovers' clearest opportunity to equalise. But after impressive dribbling to find an opening, his effort was cleared off the line by Shane Lowry.

In his team selection Appleton had confirmed the writing was definitely on the wall for Danny Murphy. Despite the manager having six players injured, and two more cup-tied, he still plumped for Anton Forrester and John O'Sullivan on the bench, two teenagers yet to make a debut, ahead of the erstwhile captain, who was told before the first instalment of this contest by Appleton that he is now "planning without him".

As this sixth-round replay and the opportunity to face Wigan at Wembley next month wandered away from Rovers, the manager may have wished for the experience of Murphy to bring on as a replacement to try and spin the match round. Asked about this, Appleton was adamant: "If there was one place we didn't struggle tonight it was the middle of the park."

Jackett now has a chance to emulate Dennis Wise as a Millwall manager who has led the club to an FA Cup final. If Jackett does so the Lions will almost certainly be in Europe again, as they were the following season after Wise's men lost the 2004 showpiece 3-0 to Manchester United.

Blackburn Rovers (4-4-2): Kean; Lowe, Dann, Hanley, Marcus Olsson (Gomes, h-t); King (Forrester, 74), Pedersen, Dunn, Martin Olsson; Rhodes, Best.

Subs not used: Sandomierski, Givet, Rekik, Goodwillie, O'Sullivan.

Millwall (4-5-1): Forde; Dunne, Shittu, Beevers, Lowry; Keogh, Trotter, Smith, Taylor, N'Guessan (Abdou, 64); Hulse.

Subs not used: Taylor, Marquis, Tyson, Smith, Osborne, Saville.

Yellow cards: Shittu (42), Dunne (44), Keogh (60).

Referee: Mark Clattenburg. Attendance: 8.635.

Man of the match: Danny Shittu.