Werder Bremen captain Max Kruse described Bayern Munich's winning penalty in the DFB-Pokal semi-final as "ridiculous".
Quickfire goals from Yuya Osako and Milot Rashica had drawn Werder level on Wednesday after Robert Lewandowski and Thomas Muller scored to put Bayern in control.
But with 10 minutes to go at Weser-Stadion, Theodor Gebre Selassie's challenge on Kingsley Coman resulted in referee Daniel Siebert pointing to the penalty spot, with VAR not used.
Lewandowski stepped up to convert and in the 91st minute ex-Bayern striker Claudio Pizarro missed a good headed chance at the back post to force extra time.