The fan, wearing a Hamburg top, stormed onto the pitch in second-half stoppage time, approached the Frenchman and slapped him in the face with a Hamburg scarf.
He then had time to make an obscene gesture before being caught by security and escorted out at the end of an otherwise peaceful and entertaining encounter.
"The club distances itself from the alleged 'HSV fan'," Hamburg said in a statement on Thursday.
"He was handed over to police. The club has already filed a complaint and will also issue a stadium ban for the man."
Hamburg had already apologised late on Wednesday to Bayern and their player via Twitter.
(Reporting by Karolos Grohmann, editing by Julien Pretot)
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