The German football federation (DFB) ruled on Friday the Hamburg team had failed to protect match officials in a game against Schalke 04 which saw coins and lighters also thrown before the linesman was struck by the cup.
Hosts St Pauli were down to nine men and trailing 2-0 to Schalke last Friday when someone in the crowd threw the cup and the linesman was struck on the back of the neck in the 87th minute. The match was then abandoned.
The DFB's disciplinary committee had ruled on Tuesday that the 2-0 result would stand.
Promoted last season, St Pauli are 17th in the 18-team table with 28 points, trailing VfL Wolfsburg on goal difference.
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