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The win on a wet night in Bremen put Bayern 10 points clear of second-place Borussia Dortmund, which can earn a maximum of nine points from its three remaining games.
Werder kept Bremen at bay for most of the first half but the champions still found a breakthrough.
Jerome Boateng played a perfectly weighted ball over the defense in the 43rd minute for Robert Lewandowski to control on his chest and hit past the goalkeeper for his 31st Bundesliga goal this season.
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Goalkeeper Manuel Neuer made a crucial late save to stop Yuya Osako’s header.
Bayern powered to its 30th German title with a perfect record of seven wins in the Bundesliga since it resumed last month in empty stadiums amid the coronavirus pandemic.
Hansi Flick has coached Bayern to 26 wins from 29 games in all competitions since he took over in November.
Bayern is chasing a possible triple. It can add the German Cup if it beats Bayer Leverkusen in the July 4 final and is in contention for the Champions League.
Europe’s premier club competition was postponed because of the coronavirus but is due to finish in a tournament format in August. Last-placed Paderborn was relegated after losing 1-0 Wednesday to Union Berlin.