Lewandowski has scored 33 goals in just 30 Bundesliga games this season, his last two games in the first half at Allianz Arena as Bayern took a 3-1 advantage at the break. There were no other scores in the second half.
Gabonese star Aubameyang scored 31 goals in the 2016/17 season for Borussia Dortmund before joining his current Arsenal club in the English Premier League.
With only one round remaining, Lewandowski is still short of the all-time remarkable record of 40 by legendary Bayern Munich and German striker Gerd Mueller in the 1971-72 season.
But with 48 goals in 41 games in all competitions this season, Lewandowski has plenty of opportunities to improve his overall record as Bayern face Bayer Leverkusen in the German Cup final on July 4 before continuing their quest to win the Champions League which will resume in August. .
Lewandowski is the top scorer in European elite competition this season with 11 goals in six games, his last against Chelsea in the first leg of the last 16 games Bayern won 3-0 at Stamford Bridge in February.
Haaland double
Meanwhile, the other most prolific goalscorers in the Bundesliga clashed as Timo Werner's RB Leipzig welcomed Erling Braut Haaland's Borussia Dortmund.
Haaland, 19, who has also been linked to several of Europe's biggest clubs, has scored 13 goals in 14 games since arriving in Dortmund from RB Salzburg last December.
Werner remains on 26 for the Bundesliga season, just behind Lewandowski.
The consolation for Leipzig, which is through the last eight of the Champions League, was the 2-0 defeat of Bayer Leverkusen at Hertha Berlin.
He left Leverkusen three points behind Leipzig in the battle for next season's automatic qualification spots for the Champions League with only one round remaining and a much smaller goal difference.
Elsewhere, it looks dismal for Werder Bremen, with a 3-1 defeat at Mainz, leaving the second lowest on the north side and two runs adrift from Fortuna Dusseldorf, who is in the relegation qualifiers.
Brighton stuns Arsenal
Meanwhile in the English Premier League, Arsenal d'Aubameyang suffered a second punishing loss in four days as Neal Maupay scored deep into overtime to give Brighton a 2-1 victory over the Gunners.
Nicolas Pepe gave Mikel Arteta the lead in the 68th minute at Amex Stadium with an astonishing strike, but local defender Lewis Dunk took advantage of Arsenal's suspicion at level seven minutes later.
He seemed ready to end all the squares until Aaron Connolly cleverly helped the ball to Maupay, who completed it perfectly.
This sparked an ugly incident when Maupay, who was in an aerial challenge with Arsenal goalkeeper Bernd Leno in a first-half clash that saw the German dying, was involved in a altercation with Matteo Guendouzi in a melee of players at the final whistle. .
Maupay said after the game that he had no intention of hurting Leno, but had little sympathy for the rest of his teammates, saying they had "what they deserved" for not showing more humility after Pepe's first goal.
Earlier, relegation wrestlers Watford scored a breathtaking equalizer to deny third place in Leicester City in a 1-1 draw on Vicarage Road.
English side back Ben Chilwell seemed to have given the visitor victory with a superb left foot strike in the 89th minute, but Craig Dawson recovered a precious point for the Hornets with an acrobatic goal over a minute later .
