Jamal Musiala, Thomas Muller and Leroy Sane set out up top for the Bavarians, who also included Serge Gnabry, Corentin Tolisso and Joshua Kimmich as their other switches.
It was all systems go for the treble champions who bagged the opener inside 14 minutes when a goalkeeping error allowed Gnabry to pick up the pieces and finish amidst calls for offside.
Gnabry had a chance to get a second before the half-hour mark from a knockdown by Thomas Muller following good work from Kimmich, but the effort sailed wide.
Kiel drew level in the last seven minutes of the half when a ball high up the field found Fin Bartels who took a few touches before riffling into the bottom-corner.
Musiala looked to restore Bayern's advantage a little later following a snap shot from inside the box, but Ioannis Gelios made light work of the former's threatening strike.
Bayern did regain the lead two minutes in the second half when Sane stepped forward to send a free-kick from 25 yards out into the top corner.
Bayern were denied a third moments later after Gelios pushed a rasping shot from the area by Musiala onto the post, as Sane made way for Douglas Costa and Musiala for Robert Lewandowski.
As a Bayern victory loomed, Kiel pulled a rabbit out of the hat when Hauke Wahl got on the end of a ball in the area to head home and send the match to extra-time right at the death.
Kimmich nearly restored the Bavarians lead minutes in with a speculative shot in the area hitting the crossbar, while Gelios thwarted Alphonso Davies later on as the match went to a penalty shootout.
Kiel held their nerve during a lengthy shoot-out to overcome the holders in sudden deah, as Bartels netted the winning kick after Marc Roca failed to score.