The visitors broke the deadlock as early as the ninth minute from the penalty spot. Sokratis Papastathopoulos's foul on Robbie Kruse saw the referee point to the spot, and Jens Langeneke made no mistake from 12 yards.
Werder began to dominate proceedings thereafter and created a number of chances during the remainder of the first half.
Werder were reduced to 10 men on 77 minutes when Assani Lukimya-Mulongoti was sent off for a second bookable offence.
However, five minutes later the home side wrapped up the points with their second goal of the afternoon, courtesy of a Kevin De Bruyne shot from inside the area.