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Kohfeldt was relieved of his duties following Sunday's (AEST) 2-0 defeat to Augsburg, Werder's eighth in nine league games.
Having taken one point from a possible 27, Werder are in the relegation play-off spot, a point adrift of Arminia Bielefeld and one ahead of Cologne, meaning they can still be automatically relegated to the 2. Bundesliga.
Kohfeldt helped Werder avoid the drop last season as they narrowly came through a play-off with Heidenheim.
But he will not have the chance to secure safety this time around, with Werder installing legendary coach Schaaf for the final game of the season against Borussia Monchengladbach.
Schaaf's first spell as coach lasted from 1999 to 2013 and saw him lead Werder to a Bundesliga and DFB-Pokal double in 2003-2004.
He won six trophies in that stint and also guided Werder to the UEFA Cup final in 2009.
"Unfortunately after the game in Augsburg, we were no longer convinced that we would be able to stay up with Florian Kohfeldt," said sporting director Frank Baumann.
"We are happy that Thomas is taking on this task in such a precarious situation for the club.
"We hope that he can bring his experience to the table and get the players ready for the last game of the season."