The Schwarzgelben will be keen to avoid four successive Champions League games without a win, while seeking revenge on the French side for 2011-12.
The Germans remain unbeaten in the Bundesliga this season, however, they will be wary of a Marseille side that won both meetings between the two sides in the 2011-12 edition.
Dortmund also slipped to a 2-1 defeat against Napoli in the club's opening game of this year's competition, with coach Jurgen Klopp sent to the sidelines after berating the fourth official in the aftermath of Gonzalo Higuain's opening goal at the Stadio San Paolo.
Klopp has been handed a one-match ban as a result of his actions in Naples but, with Dortmund in fine domestic form, last year's finalist should be confident of atoning for that defeat even with the trainer banished from the dugout.
Dortmund is likely to go in as the favorite for the game at Signal Iduna Park, but will have to try and seal the points without goalkeeper Roman Weidenfeller, who is suspended after being sent off in the loss to Napoli.
Midfielders Sebastian Kehl (foot) and Ilkay Gundogan (back) are also unavailable, as is defender Lukasz Piszczek (hip).
Marseille will be hopeful of replicating the results it achieved back in 2011, but will need to improve on a disappointing performance in the opener against Arsenal, which the club lost 2-1 despite creating a number of chances.
Still, Baup's side heads into the contest on the back of a confident 2-0 win at Lorient last Saturday and will look to the likes of Mathieu Valbuena and Andre Ayew to break down the Dortmund defense.
However, the Provence outfit could well be without Andre-Pierre Gignac - top scorer with 18 goals last term - as he continues to struggle with a toe injury, while Jeremy Morel (knee) is also a doubt.