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Patrick Owomoyela put the visitors in front after 11 minutes when he headed home Alexander Frei's cross.
Paraguayan forward Nelson Valdez sealed the victory nine minutes after the restart with a right-footed shot.
Egypt forward Zidan once again started on the bench before being introduced in the 78th minute instead of Swiss striker and Dortmund top scorer Frei.
The 27-year-old, who joined Jurgen Klopp's side from Hamburg last summer, scored five league goals so far this season.
Dortmund moved into seventh place on 46 points, three behind a Europa League place (the new version of the UEFA Cup).
Elsewhere, Wolfsburg maintained their position on top of the table with a 2-1 victory over Bayer Leverkusen.
A brace by in-form Brazilian striker Grafite, who took his tally to 22 goals, gave Wolfsburg all three points to maintain their three-point advantage over Bayern Munich, who beat Arminia Bielefeld 1-0.
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