The 17-year-old headed in the far post in the 79th minute to take Dortmund to the top on 15 points.
There was bad news for the hosts, however, as their captain Marco Reus was carried away with what appeared to be a serious ankle injury.
The Germany international, who was called up this month for the Nations League games against Hungary against England, had sprained his ankle in the 32nd minute.
Reus sat out Germany’s 2014 World Cup-winning run after being injured in their final warm-up match before their departure to Brazil. He also missed Euro 2016 due to injury.