Allofs this week accepted an offer from Bundesliga rivals Wolfsburg to take over as their director of sport, leaving Schaaf alone at the wheel for the first time in over a decade.
"I just have to accept the situation, which is not very pleasant," said Schaaf. "Klaus wanted to go in a new direction and that's fine.
"There are always changes in football and now there is a change at Werder Bremen.
"I know that it was hard for Klaus to break the news to me. As soon as I got to know that he was thinking about (moving to Wolfsburg), I already knew how things would end because I've known him long enough."
Schaaf did not want to dwell on the past too much, though, and is instead focused on guiding Bremen to victory over Dusseldorf on Sunday.
"I will carry on doing my job the way I have always done it," he added on his club's website.
"We had already given thought to possible transfers in the winter and that does not change just because of this move.
"Our squad rebuilding is in full flow and that is not something which is only a short-term measure.
"It's important for me that things now move on. We are fixated on this game, which we want to bring to the successful result, which we need."
Fortuna also need a successful result after a run of seven games without a win, a period in which they have conceded 16 goals after keeping five clean sheets at the start of the campaign.
"The important thing is that we don't let our heads drop," said coach Norbert Meier, who will recall Andrea Lambertz to his side after leaving him out last weekend.
"He took my decision very professionally last week. Lambertz didn't take it personally."