In the 1989 summer, Rufer signed with SV Werder Bremen, coached by Otto Rehhagel. His Bundesliga debut came on 29 July, in a 0–0 draw at FC St. Pauli, and his impact was immediate, as he netted six times in his first 13 league matches. Overall, he would play an enormous part in the side's achievements, pairing with Klaus Allofs up front: on 6 May 1992, both scored in the final of the season's UEFA Cup Winners' Cup, in Lisbon (2–0 win against AS Monaco FC).