Bayern lacked fluency in the opening stages despite scoring 13 goals in their previous three Bundesliga games, but did enough to edge closer to an eighth straight title.
German health minister Jens Spahn on Sunday called for the cancellation of all gatherings of more than 1,000 people in the country over fears surrounding the spread of the new coronavirus.
But the German league immediately reacted, insisting that it was "out of the question" that the season would be delayed beyond its scheduled finish on May 16, a week before the German Cup final.
Cases of COVID-19 in the country reached more than 850 on Sunday. Bayern extended their unbeaten run to 15 games despite starting slowly and just by Muller's brace they finally got the win.