The Poland striker showed clinical finishing to tuck away an Alphonso Davies second-half pass at the Allianz Arena and claim his 13th league goal and set a new record for scoring in the first nine Bundesliga games of the season.
Lewandowski, on the mark in each of his last 13 games for Bayern, overtook the previous league record set by current Arsenal forward Pierre-Emerick Aubameyang who scored in each of the first eight games of the 2015/16 season for Borussia Dortmund.
"I'll try to keep playing like this, there are still a lot of games to come," said Lewandowski, currently on course to break Gerd Mueller's record of 40 league goals.
"You have to be in shape all season. I don't think about how many goals I've scored, I'm just trying to get us the three points."
Lewandowski had also scored twice in Bayern's 3-2 midweek win at Olympiakos in the Champions League and he now has 19 goals in just 14 appearances in all competitions during what is turning into the best season of his career.
Defensive woes blight Kovac as Bayern host minnows Union
He is already the top-scoring foreigner in Bundesliga history with 215 league goals for Bayern and former club Dortmund.
Defender Benjamin Pavard gave the hosts the lead before Lewandowski's second just after the break.
Bayern captain Manuel Neuer saved a Sebastian Anderson penalty on 59 minutes and not to be outdone, Union's Poland goalkeeper Ralf Gikiewicz denied Bayern winger Serge Gnabry from close range.
Lewandowski looked to have claimed a second, but his effort six minutes from time was ruled out.
Union grabbed a late consolation goal when replacement striker Sebastian Polter netted from the penalty spot having been brought down by Pavard.
Munich can lose top spot Sunday to previous leaders Borussia Moenchengladbach, who host Eintracht Frankfurt, and Wolfsburg who can leap-frog Niko Kovac's Bayern by beating Augsburg at home.
Dortmund moved up to third after a goalless draw at Schalke, who had the better chances in the Ruhr derby.
Schalke centre-back Salif Sane headed onto the crossbar with nearly half an hour played and soon after midfielder Suat Serdar hit the post.
Schalke's Wales forward Rabbi Matondo, 19, wasted three clear chances, while at the other end Dortmund playmaker Marco Reus and England winger Jadon Sancho went close for the visitors.
"We didn't score, but in the first half we had two big chances," said Schalke captain and goalkeeper Alexander Nuebel.
Benched Mueller admits frustrations amid Bayern exit reports
"If one goes in, things looks different. It was difficult for them to score, because there was nobody who wanted to get into the box."
Dortmund's Reus admitted things are not clicking for his team.
"The ease will only come back when we're aggressive, when we follow through our plan and win games," said the 30-year-old.
"That's not there at the moment. We have to be able to get it back. We are not on PlayStation here."
Freiburg are a point behind Bayern in second after bouncing back from last weekend's shock defeat at Union to earn a 2-1 win at home to RB Leipzig.
After beating Zenit Saint-Petersburg in the Champions League in mid-week, Leipzig came unstuck as Nicolas Hoefler gave Freiburg the lead on the stroke of half-time before striker Nils Petersen came off the bench to add a second on 90 minutes.
Lukas Klostermann scored a consolation goal for Leipzig.
On Saturday night, Bayer Leverkusen missed the chance to go third when they were held to a 2-2 draw at home to Werder Bremen as Lucas Alario grabbed the second-half equaliser for the hosts.
Bottom side Paderborn earned their first win this season as defender Sebastian Schonlau and midfielder Abdelhamid Sabiri scored in a 2-0 win at home to Fortuna Duesseldorf.
Mid-table Hoffenheim earned their third straight success, having beaten Bayern and Schalke, with Benjamin Huebner scoring late in their 3-2 win at Hertha Berlin.
COMMENTS
Comments are moderated and generally will be posted if they are on-topic and not abusive.
For more information, please see our Comments FAQ