The two sides meet for the fourth time this campaign with the Lions having the edge, particularly after their triumph over Rovers in the quarter-final of the FA Cup last month.
The Lancashire club return to the Den in search of important points and with Millwall still not safe themselves it could be a tense affair.
"There was a lot of disappointment from the players in not getting to Wembley and we have to use that as a motivation along with the desire to stay in the Championship," said Bowyer.
"It is a different game entirely and we just have to make sure that we are back to the level of performance that we showed against Derby and Huddersfield.
"The players know and I know, that we can produce better than we showed in the second half at Watford.
"You look at the two games that we played previously and the level of our performance in them, the players know they can do better.
"That is what we'll be stressing to the players, we just have to keep going."
Tickets for the match will be on sale from the Den on the day of the game priced £26 Adults, £17 for Seniors over 60, £13 for Under 16s and £7 for Under 12s.