Thomas Muller has apologised to Bayern Munich supporters following his side's "catastrophic" 5-0 thrashing at the hands of Borussia Monchengladbach on Wednesday.

Bundesliga champions Bayern were three goals down inside 21 minutes and conceded twice more before the hour mark in the DFB-Pokal second-round tie.

The heavy defeat at Borussia-Park marks the first time Bayern have lost a game by at least five goals since December 1978 in a Bundesliga clash with Fortuna Dusseldorf.

Muller played a full part in the Bavarian giants' heaviest loss in 43 years and was taken aback by the manner of his side's performance, which came despite a strong line-up being fielded.

"We never got to the point where our Bayern engine kicked in," he said. "We can only apologise to the fans and apologise to Gladbach. 

"With the exception of [Manuel] Neuer, it was a catastrophic performance from us.

"I haven't experienced anything like that before. It's difficult to wrap your head round. We have to put it behind us now, because we've got a game on Saturday."

Bayern had scored in their previous 83 competitive matches in a run spanning back to February 2020, which includes 60 goals in 15 games in all competitions this season – at least 17 more than any other side in Europe's top five leagues,

The visitors were pulled apart at the back, with Ramy Bensebaini and Breel Embolo helping themselves to a couple of goals each after Kouadio Kone's early opener.

Bayern's loss came in the absence of head coach Julian Nagelsmann, who is continuing to isolate at home after testing positive for coronavirus.

Stand-in boss Dino Toppmoller oversaw Bayern's biggest ever cup defeat and is aware of the importance of hitting back with victory at Union Berlin in Saturday's Bundesliga clash.

"It was an absolutely bad day. I'm sorry that we disappointed our fans today," he said at his post-match news conference.

"We were in constant contact with Julian. We prepared the game plan together and discussed the lineup via FaceTime. 

"I don't think it was a system problem – it was just a dark day and we were late to every ball. It's difficult to accept now but we've to show a reaction."

Bayern have now failed to reach the last 16 of the DFB-Pokal in back-to-back seasons for the first time since between 1994 and 1996, having suffered a shock loss to Holstein Kiel at the same stage last year.

Bayern Munich head coach Julian Nagelsmann has tested positive for COVID-19.

Nagelsmann was absent due to 'flu-like symptoms' as Bayern beat Benfica 4-0 in Portugal on Wednesday, maintaining their flawless Champions League group-stage record so far this season, with assistant manager Dino Toppmoller standing in.

The Bavarian giants have won each of their first three games in the competition, scoring 12 times and not conceding a single goal to sit five points clear at the top of Group E.

The club confirmed on Thursday morning that the 34-year-old, despite being fully vaccinated, had tested positive for the virus and will return to Munich separately instead of with the rest of the squad before isolating at his home.

As a result, Nagelsmann will miss Bayern's next league game at home against Hoffenheim on October 23, with Toppmoller set to continue filling in.

Bayern are one point ahead of Borussia Dortmund at the top of the Bundesliga, winning six and losing just one of their first eight games as they seek a 10th consecutive league title.