Elsewhere, runner up Borussia Monchengladbach suffered a setback as Hertha Berlin snatched a 3-0 away victory on the goals from Salomon Kalou, Ondrej Duda and Davie Selke.
"When you lead 3-0 at home and then you play a 3-3 then it obviously is extremely bitter", Goetze told reporters.
Borussia Dortmund's Mario Goetze was also on target on Saturday for his 50th league goal in the match against Hoffenheim but the league leaders wasted a three-goal lead.
He has now scored three times and set up another four goals in the Bundesliga this season.
But the 18-year-old's joy was cut short when forward Lewandowski struck two minutes later to Bayern ahead once more.
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Bayern, which slumped to a 3-1 defeat at Bayer Leverkusen last weekend, bounced back with a comprehensive defeat of Schalke, which could easily have lost by more.
This is a game that Dortmund had complete control of and should never have dropped points.
The shock result came after the table toppers completely dominated for more than an hour.
First captain Marco Reus injured his thigh and then coach Lucien Favre was forced to miss Saturday's Bundesliga home game with Hoffenheim with illness.
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The England global then set up Mario Gotze for Dortmund's second goal before combining with Gotze to set up Raphael Guerreiro for an easy tap-in in the 66th.
Sancho opened the scoring, set up two goals and hit the post as the host dazzled over 70 minutes at Signal Iduna Park.
Pavel Kaderabek rose above his marker to head in with seven minutes left and set up a nervous finale.
"The club had shown with a player like Christian Pulisic that they were going in the right way, playing youngsters and giving them a chance", Sancho said.
Hoffenheim netted three times in eight minutes to seal an unlikely comeback meaning Borussia Dortmund's lead at the top was still only eight points. "Especially after such a performance for large parts of the game and after a strong first half".
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