"It's something special. A derby win at this point in the season is a highlight", Schalke sporting director Christian Heidel said. "It was a deserved victory".
Even some of the Dortmund faithful couldn't hide their appreciation.
Schalke won the game 2-0 thanks to goals from Yevhen Konoplyanka and Naldo but the injury to Batshuayi is a more pressing concern.
With the result, runners-up Schalke opened up a four-point gap to third-placed Bayer Leverkusen, while Dortmund slipped into 4th place.
"We need to look at what went wrong in the first 45 to 60 minutes today", Reus told Sky.
"We played a great first half".
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Konoplyanka had the beating of Burki on the stroke of half-time after cutting in from the left, but his strike flew inches past the far post.
Yet with eight minutes to play, Schalke were awarded a free-kick around 30 metres from goal.
As the match progressed, Dortmund pressed passive Schalke into the defense.
Dortmund's disappointing afternoon ended with Michy Batshuayi being stretchered off in injury time.
Elsewhere, Leipzig and Werder Bremen shared the spoils following a 1-1 draw. Max Kruse's curling shot struck the bar, and Niklas Moisander scuffed the ball in on the rebound.
Schalke cut a better figure in front of the goal as Naldo secured all three points after unleashing 28-meter hammer past Dortmund goalie Roman Buerki in the closing period of the derby.
With Leipzig looking beaten at half-time, Ralph Hasenhuettl brought on Lookman, who promptly equalised.