The striker has now scored 40 goals in 28 league games this season.
Muller averaged a goal every 77 minutes when he set the Bundesliga record in 1972 but Lewandowski did so with an average of a goal every 58 minutes.
He has netted in 18 of his past 19 Bundesliga appearances.
The only team during that run Lewandowski failed to score against was Hertha Berlin on 5 February.
Lewandowski celebrated the goal by lifting up his playing top to show a T-shirt underneath with Muller’s face on and the words “4ever Gerd”.
His team-mates then quickly formed a guard of honour near the touchline opposite staff members while Lewandowski celebrated with his arms outstretched.
The Poland international is the first player to reach 40 goals in a single season in one of Europe’s top five leagues since Luis Suarez for Barcelona in 2015-2016.
Lewandowski’s record-equalling goal came from the spot in the 26th minute to put champions Bayern ahead before SC Freiburg defender Manuel Gulde equalised three minutes later.
Ex-Manchester City winger Leroy Sane restored Bayern’s lead in the second half but defender Christian Gunter made it 2-2. Lewandowski missed a golden opportunity to break the record late on.
Bayern were crowned champions of Germany for the ninth straight season after Lewandowski’s hat-trick helped them thrash Borussia Monchengladbach last week.
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