Bayern lost Franck Ribery to a worrying ankle injury soon afterwards before Belgian international defender van Buyten cropped up in the first minute of added time to score the clincher.
Ribery's long-range shot had set up Mueller's equalizer and Bayern will be hoping he will be fit to face Basel in next Tuesday's Champions League group clash.
Manager Louis van Gaal said the injury was a worrying development.
"It doesn't look good, it looks like it is a bad ankle injury and we will have to wait and see what the tests show," he told AFP.
Bayern made the worst possible start with midfielder Sebastian Rudy finding Ibisevic to score after just 36 seconds, the fastest goal in Hoffenheim's short history.
The eventual victory lifts van Gaal's men into seventh place with eight points from five games, while Hoffenheim stay in second.
Early leaders Mainz continued their storming start to the season Tuesday with a 2-0 win over Cologne to make it five wins from five matches.
The hosts took the lead through Lewis Holtby after 72 minutes and the midfielder scored his second in added time.
But Champions League hopefuls Werder Bremen crashed to a second straight Bundesliga defeat when they were thrashed 4-1at Hannover.
After defeat by Mainz at home on Saturday, it is hardly ideal preparation for their match against defending champions Inter Milan in Italy next Wednesday.
Bremen fell behind to an own-goal by Germany defender Clemens Fritz after just 10 minutes but Torsten Frings equalized from the spot before halftime.
But second half goals from Didier Ya Konan, Christian Schulz and Mohammed Abdellaoue secured an easy Hannover victory.
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