The visitors thought they had a penalty before the break when Deniz Aytekin pointed to the spot after Werner fell under Albin Ekdal's challenge. Aytekin consulted his video assistant, however. TV replays showed Ekdal got the ball before making contact with Werner's foot and the decision was reversed.
Naby Keita finally broke the deadlock with a fine strike from distance midway through the second half. Hamburg coach Markus Gisdol brought on Sven Schipplock for a defensive midfielder and the move almost paid off immediately when Peter Gulacsi produced a brilliant save to deny the Hamburg forward an equalizer.
The home side was to rue the miss when Werner scored on the counterattack. Kevin Kampl sent the Germany striker through to race forward and the 21-year-old stayed cool in a one-on-one with the goalkeeper.