The bans come ahead of Saturday's World Cup qualifier in Glasgow where England will travel to face old rivals Scotland.
The two fans have received lifetime bans from the England Supporters Travel Club (ESTC), the official organisation for away support, the FA confirmed on Wednesday.
The ESTC is the exclusive provider of tickets for the away end at England matches and tickets must be picked up in person in the foreign city.
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One of the banned fans was seen making a Nazi salute towards German supporters while another was viewed imitating an Adolf Hitler moustache and cut-throat gestures.
Another 25 supporters have been given bans and suspension of various lengths due to their behaviour in Dortmund.
The behaviour of England fans during the March game, where they taunted German supporters about World War Two, was widely criticised by British media.
(Reporting by Simon Evans; editing by Sudipto Ganguly)
