Kenny Jackett's side see off a wasteful Rovers side at Ewood Park to advance to the FA Cup semi-finals, where they will face Wigan for a place in the showpiece
The former Nigeria international headed home Liam Trotter's corner in the 42nd minute to set up a semi-final meeting with Premier League side Wigan Athletic at Wembley.
The Lions made no changes from Saturday's initial tie, while Michael Appleton brought Martin Olsson and David Dunn in for Adam Henley and David Bentley.
It was Blackburn that looked the liveliest in the early stages, with Leon Best and Jordan Rhodes both trying their luck from distance with neither really testing David Forde in the Millwall goal.
The first real goalscoring opportunity came after 16 minutes, when Morten Gamst Pedersen played a low corner to Dunn on the edge of the box, who curled his first-time shot just past the left-hand post.
Millwall finally came alive midway through the first half and managed their first shot at the home side’s goal, when midfielder Chris Taylor fired well over from range.
As the first-half progressed, Rovers continued to pile pressure onto the Millwall back four but Joshua King and Pedersen were both guilty of wasting good scoring openings.
As the sides looked to be heading into the break all square, Millwall struck the first blow.
Liam Trotter’s out-swinging corner was met by the head of Shittu, who climbed above Best and nodded the ball into the ground and the back of the net to give the Lions the advantage at half-time.
Blackburn made one change at half-time; introducing Portuguese striker Nuno Gomes in place of the disappointing Marcus Olsson.
The hosts piled pressure onto the Lions in the second half, with Shittu coming to his side's rescue once again to clear Best's shot off the line with Forde well beaten.
Best again spurned a gilt-edged chance with time running out, firing over the bar from inside the box as the Lions clung on to their precious win.