The Bavarians have a gruelling fixture list of nine games in 29 days in April, including playing Real Madrid home and away in their mouth-watering Champions League quarter-final.
High-flying Hoffenheim deals Bayern its 2nd Bundesliga loss.
Hoffenheim head coach Julian Nagelsmann has compared the feeling of beating Bayern Munich to being "like a drug".
It was Hoffenheim who stopped Bayern Munich's run by reaping their first victory in 18 encounters between the two sides.
"It was better in the second half, but the ball wouldn't go in".
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After thumping Augsburg 6-0 on Saturday, Bayern are unbeaten in their last 20 games dating back to November, but play third-placed Hoffenheim then host arch-rivals Borussia Dortmund, who are fourth, on Saturday.
Hoffenheim captain Sebastian Rudy and fellow defender Niklas Suele were playing against their future club after agreeing to switch to Bayern for next season.
The Bundesliga leaders threw everything forward in the closing stages of the second half, but the host managed to hold on for an impressive three points.
While Lewandowski's efforts to add to his tally of 24 goals were frustrated in Sinsheim, Pierre-Emerick Aubameyang rounded off the scoring in Dortmund to take his total to a league-leading 25.
"On one hand, we're happy with the clear win and the performance". We had our chances to level the scores.
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Dortmund created a number of opportunities, but Rene Adler denied Aubameyang several chances to extend the lead.
Dortmund wrapped up the victory with two goals in the last 10 minutes.
Hamburg are only just clear of the relegation places, but are unbeaten in their last four league games after Lewis Holtby scored their 92nd-minute victor in Saturday's 2-1 victory against Cologne. The first half was unnecessary.
Four minutes later, Kruse crossed for Maximilian Eggestein to seal it.
Merkel was there to see the home side wearing jerseys highlighting an initiative supported by around 180 companies to promote the integration of refugees into the workplace.
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