The match was supposed to have been played on Aug. 6 but it was postponed due to a number of coronavirus infections among the Bremen-based team’s players.
Captain Marco Reus was involved in all four goals on Thursday as Dortmund won the cup for the fifth time and denied bitter rival Leipzig a first title.
Haaland, 20, has been sidelined by deep bruising which saw him miss Dortmund's semi-final thrashing of second-tier Holstein Kiel and Saturday's 3-2 league win over Leipzig.
A first-half goal from Guido Burgstaller fired Schalke to a 1-0 victory over Wolfsburg and a place in the semi-finals of the German Cup.
Isak shone for holders Borussia Dortmund in their 5-0 German Cup second-round romp at third-division Magdeburg.
In 2013 Jupp Heynckes steered Bayern Munich to the treble of Champions League, German Cup and Bundesliga titles.
Should Dortmund reach the last four, it will set up a repeat of last year's final, which Bayern won on penalties.
Robert Lewandowski took his season tally to 30 goals to inspire Bayern Munich's 3-0 win over ten-man Schalke.