That put Lewandowski two clear of his nearest rival, who ironically enough is the man whose place he will take at Bayern - Mario Mandzukic.
Dortmund were comfortably in control of second place behind runaway champions Bayern, who beat Stuttgart 1-0.
Hamburg SV, the Bundesliga's only ever-present club, escaped direct relegation by the skin of their teeth on Saturday after a 3-2 defeat at Mainz 05 sent them into a two-leg playoff against a second division team.
Hamburg, who have never been relegated in the Bundesliga's 51-year history, clung on despite losing their last five games, helped by equally poor form from their rivals.
Nuremberg and Eintracht Braunschweig, who started the final day of the league season below Hamburg but could have moved above them with wins, were relegated after losing 4-1 at Schalke 04 and 3-1 at Hoffenheim respectively.
Nuremberg lost their last seven while Braunschweig, who went straight back down after being promoted last season, also ended with five consecutive losses.
Hamburg, the so-called Bundesliga Dinos (dinosaurs), finished 16th with 27 points ahead of Nuremberg on 26 and Braunschweig with 25.
Schalke 04's victory clinched third place and sent them straight into the Champions League group stage next season, while Bayer Leverkusen finished fourth with a 2-1 triumph over Werder Bremen to qualify for the playoff round.
Leverkusen edged out VfL Wolfsburg, 3-1 winners over Borussia Moenchengladbach, by one point. Wolfsburg, Moenchengladbach and Mainz qualified for the Europa League.
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- Hamburg SV