The UEFA Super Cup pitches the winner of the Champions League against the winner of the Europa League and it was an even contest that needed extra time before a winner could emerge.
Javi Martinez turned out to be the hero as he was in the right place at the right time to deliver the decisive goal in extra time.
Bayern started on the backfoot after Lucas Ocampos gave Sevilla a 1-0 lead from the penalty spot in the 13th minute.
The referee judged David Alaba to have fouled Ivan Rakitic in the 18-yard box, a decision that was upheld after a video review.
Ocampos was on hand to take the resultant kick and he did well; sending Manuel Neuer the other way with a no-look shot into the bottom left corner.
Bayern pressed for an eqauliser afterwards and after coming close on a number of occasions, they restored parity in the 34th minute through Leon Goretzka.
Robert Lewandowski played a vital role in the equalizer when he expertly drew the attention of three Sevilla players before laying off a perfect pass back for Goretzka.
Chances came for both teams afterward and even goals were chalked off thus making the match extend into extra time.
The decisive moment came in the 104th minute when Sevilla keeper Yassine Bounou made a save on a shot by David Alaba from a Bayern corner but failed to clear the danger thus given Martinez the chance to head in the winning goal.
The next stop for Bayern is an away game against Hoffenheim on Sunday in the Bundesliga. On the same day, Sevilla open their La Liga campaign away at Cadiz.