Rebic had broken the deadlock in the first half before Bayern equalised through their star striker Robert Lewandowski.
However, the Bundesliga champions would find themselves a goal down again with less than ten minutes remaining on the clock. Although it wouldn't be without its controversy.
Rebic chased down a long ball, and used his strength once again to shake off the two Bayern centre-backs, before dinking a wonderful finish over Sven Ulreich.
As he ran off to celebrate what might be the winning goal, the Bayern players surrounded the referee claiming a handball in the build-up.
He would send it up to VAR but after careful analysis, the on-field decision stood and Frankfurt were on their way to famous victory in manager Niko Kovac's final game in charge.