Wolfsburg defeated Preussen Munster 3-1 after extra-time on August 8 but the Bundesliga side, who had made five substitutions in normal time made another change when the game travelled for another 30 minutes, contrary to the rules.
The extra change by manager Mark Van Bommel went unnoticed by the match officials and Preussen Munster officials launched a protest after the game which has now gone in their favour.
Munster have been awarded a 2-0 victory and will progress to the second round of the DFB-Pokal.
Announcing the German Football Association(DFB) sports court's decision on Monday, deputy chairman Stephan Oberholz commented: "The clubs are responsible for substitutions. One of their basic obligations is to find out about substitution options and to act accordingly.
"VfL Wolfsburg has a duty against this violated and thus frivolously and avoidably committed the central error in the inadmissible sixth substitution process.
"The club cannot invoke exonerating negligence on the part of the referee team. It can remain unanswered whether the fourth official advised those responsible at the club incorrectly or provided inaccurate information during the exchange process.
"Even if one assumes such wrong information, the main initial error is to be blamed on the club, so that any joint responsibility of the referee resigns completely."
