Werner went to ground as he touched the ball past Schalke goalkeeper Ralf Fahrmann, who was incredulous to see the referee point to the spot.
Julian Draxler has reaffirmed his intention to leave Wolfsburg as soon as possible after being jeered by fans on Saturday.
Dortmund's thrashing of Borussia Monchengladbach earns the praise of Thomas Tuchel, who lauds his side's complete effort.
Thomas Tuchel has left the future of Marcel Schmelzer's captaincy beyond 2016 open as Maro Reus made his first league start.
RB Leipzig moved back to the top of the Bundesliga; Borussia Dortmund got back to winning ways with a 4-1 win over Borussia Monchengladbach.
Ousmane Dembele received extra praise from coach Thomas Tuchel after his performance in Borussia Dortmund's 4-1 home win.