Japan's Noriaki Kasai was third with jumps of 139.5 and 137.5 for 292.0 points.
Anders Bardal of Norway was fourth, followed by Finland's Janne Ahonen, with Japan's Taku Takeuchi and Daiki Ito sixth and seventh, respectively.
Overall leader Gregor Schlierenzauer of Austria had to be content with a share of eighth place with Germany's Severin Freund.
Saturday's winner Morgenstern landed badly on his jump of 141.0.
"He's not doing well. He's in a lot of pain and has a cut on his face," Austria coach Alexander Poitner said before the helicopter arrived. "Thomas is very calm, he can move his limbs, but everything has to be checked out ... I'm deeply sorry for him, but he's a fighter."
Schlierenzauer leads the standings with 298 points, ahead of Freund on 256 and Takeuchi on 255.