The victory was enough for Jurgen Klopp's side to claim the league title for the first time in nine years as their closest rivals Bayer Leverkusen lost to Koln by the same score-line.
Dortmund last claimed the league title in the 2001-2002 season.
Zidan didn't play a major role in their domestic campaign this season, thanks to a long-standing knee injury that kept him out of action for months.
However, Dortmund's feat made him the first-ever Egyptian to win the Bundesliga trophy.
Former Egypt defender Hany Ramzy, who's now Egypt U-20 coach, once came close to winning the prestigious silverware with Werder Bremen.
Zidan has been named in Dortmund's starting eleven only once so far this season. He has taken part in seven games overall.
He's the third Egyptian player to pull off a top-flight triumph in Europe. Previously, Mido won the Eredivisie with Ajax Amsterdam before Ahmed Hassan led Anderlecht to a Belgian Pro League title.
Zidan celebrated Dortmund's triumph along with his baby son on the pitch after the match.