Werder chief resigns over player agency links
Born, who has been chairman since 1999, denied any wrongdoing though.
"Given I am the object of reports linking me with financial transactions with the Peruvian company 'Image' I will bring forward my planned resignation," he told the club's website.
"I can assure you I have never gained any illegal financial advantages at the expense of Werder Bremen but to prove this needs some time and I want to protect the team from such an unnecessary burden."
The club said Born would be succeeded, at least temporarily, by Werder manager Klaus Allofs.
Under Born, Werder won the league and cup double in 2004.
"This (resignation) was the right decision," said supervisory board chairman Willi Lemke. "We must, for the good of Werder, create the necessary transparency in this case."
The supervisory board make sure the statutes of the club are upheld while the club board, of which Born was chairman, run day to day activities.
Werder are 10th in the Bundesliga and will take a 1-0 lead into the second leg of the UEFA Cup last-16 tie against St Etienne in France next week.