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It came after more than two months out due to the COVID-19 pandemic, and protect their four-point lead at the top.
League top scorer Robert Lewandowski converted a 40th minute spot kick and Benjamin Pavard headed in a corner in the 80th in an empty stadium, to keep the Bavarians in the driving seat for a record-extending eighth successive league title.
They are now on 58 points, with Borussia Dortmund in second place on 54 following their 4-0 demolition of Schalke 04 on Saturday. There are eight matchdays left in the season.
"We were there from the start even though it may not have been our best performance today," said Bayer captain Manuel Neuer, who has now kept a clean sheet at least once against all 35 Bundesliga clubs he has played against.
"We are happy to have controlled the game and to have brought the three points home. In games without fans the minutes are very long until the final whistle."
The Bundesliga is the first major sports league in the world to restart amid the pandemic but games are played without fans.
A set of strict health regulations are governing the matches, including a ban on spectators, limited staff inside and outside the stadium and regular testing.
The empty slabs of the concrete stands in the Alte Foersterei stadium with a few dozen officials, staff and substitutes scattered around were an unusual setting for a return to action of Germany's most successful club.
But Bayern quickly took control and had an early effort ruled offside. Union were without coach Urs Fischer, who was missing for private reasons.
The visitors had to wait until the 40th minute to score with Lewandowski, chasing Gerd Mueller's legendary 40-league goal record from 1972, grabbing his 26th of the campaign from the spot.
The game lost some of its pace after the break with the players lacking match practice.
Pavard made sure of the three points when he headed in a Joshua Kimmich corner.
Berlin police had warned fans, as in all stadiums, to stay away but said a few dozen had gathered outside the stadium prior to the game.
They left following talks with police, who had a force of 400 around the stadium.
The German Football League is desperate to avoid any rule violation that could threaten the league restart as it hopes to finish the season by June 30 for contractual reasons.