The match at the Veltins Arena – which finished 3-1 to Dortmund – was delayed as flares and smoke bombs were thrown from Dortmund's section of the crowd onto the pitch and at Schalke fans.
Dortmund goalkeeper Roman Weidenfeller had objects thrown in his direction as he pleaded for calm in front of the travelling faithful.
Eight arrests were made after trouble spilled from the stadium to the streets after the game and local police blamed the club for lax security afterwards.
As well as close to 500 people being banned from Schalke's stadium, a further 31 individuals have been given national stadium bans.
The orders will remain enforced until until June 30, 2019.
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