The Rheinoper said it was aware that the concept and its implementation would be "controversial".
"But it was with great astonishment that we noted that some scenes, in particular very realistic execution scenes, caused physical and psychological distress to a number of spectators who had to seek medical help," read a statement on the Rheinoper's website.
One scene showed a family getting undressed and having their heads shaved before being murdered by Nazi henchmen, while another made a vivid allusion to gas chambers, with naked figures in glass cubes slowly engulfed in artificial fog, German media reported.
Theatre director Burkhard Kosminki refused to make changes to the show and the opera house explained it could not continue presenting it in its current form.
The opera will instead be shown as a concert performance from Thursday.
In Wagner's original the opera takes place in Venusberg - mountain abode of the Roman goddess and a symbol of hedonistic love.
The now cancelled version transforms Venusberg into a Nazi crime scene, provoking boos from the audience 30 minutes into the premiere.
Michael Szentei-Heise, head of the Düsseldorf Jewish community said the adaptation was "in bad taste" but did not call for it to be cancelled.
He said that while Wagner was certainly an "ardent anti-Semite ... he had nothing to do with the Holocaust."
This year marks the 200th anniversary of the German composer's birth, and the bicentennial is being celebrated in various parts of the world.