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.
In the day’s first match, Cologne squandered a two-goal lead and had to sweat to rescue a point in their 2-2 draw with visitors Mainz 05.
Cologne, looking for their fourth straight league win, thought they had wrapped up the match played without spectators after early goals in each half.
Bayern 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 match days left in the season.
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.
They 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.
In the first match yesterday, despite the lack of fans, Cologne had some support as about 1,300 season-ticket holders sent in their favourite club items - team shirts, scarves or stuffed animals - which were draped over the empty seats.
Mark Uth converted a sixth-minute penalty he won himself and Florian Kainz headed in a perfect Dominick Drexler cross at the far post in the 52nd minute.
But Mainz, led by former Cologne coach Achim Beierlorzer, cut the deficit through Taiwo Awoniyi in the 61st and levelled 11 minutes later thanks to Kunde Malong’s 30-metre solo run and fine finish from inside the box. They also went close to scoring a third in the final minutes.
“I am not saying I am satisfied but we can live with the point,” Cologne coach Markus Gisdol, said.