The visitors found themselves trailing 0-2 just 15 minutes into Friday's contest at the Allianz Arena after giving up goals to Xabi Alonso and Robert Lewandowski, reports Efe.
Bayern, who beat Borussia Dortmund 2-0 two weeks ago to win the German Super Cup, give every sign of continuing their dominance of the Bundesliga under newly-appointed coach Carlo Ancelotti.
The hosts would have led 4-0 by half-time if Lewandowski hadn't wasted a pair of clear chances in the 32nd and 39th minutes.
But the Polish striker made up for his earlier lapses with a goal in the opening minute of the second half, converting a cross from Thomas Maller to make it 3-0.
Philipp Lahm scored in the 66th minute and Franck Ribery added to Werder's misery seven minutes later before Lewandowski completed the hat-trick with a goal from the penalty spot in the 77th minute.