Zidan played for 21 minutes against his former club, despite skipping Egypt's friendly draw with Guinea on Wednesday 'due to injury'.
Ex-Dortmund midfielder Guy Demel opened the scoring for the hosts as early as the third minute, but Nelson Valdez equalized instantly a few seconds later.
However, quickfire goals by Ze Roberto and Jose Guerrero in the 10th and 12th minutes left Dortmund undone.
In the 69th minute, goalscorer Valdez made way for Zidan, but HSV scored their fourth goal three minutes later, courtesy of a Marcus Berg strike.
Dortmund lie eighth with three points, while Hamburg are in charge of the table with four.
Elsewhere, newly-promoted Mainz remained undefeated as they claimed a 1-1 draw at Hannover, with Egyptian forward Gamal Hamza missing out once again.
Bayern Munich have also registered a second draw as they were held at home 1-1 by Werder Bremen.