The win moved them within four points of joint Bundesliga leaders RB Leipzig and Borussia Moenchengladbach.

The 18-year-old Zirkzee came on in the 90th to score off Gnabry, and the Germany forward then wrapped up matters as the champions stole an improbable victory.

Robert Lewandowski had opened in the 16th for a league-leading 19 goals and outright third place in the Bundesliga all-time list with 221 goals, moving ahead of Jupp Heynckes. Vicenzo Grifo got Freiburg's equaliser in the 59th.

Bayern moved into third place with 30 points, four behind Leipzig and Gladbach, with Gladbach winning 2-0 over bottom side Paderborn on the day, after Leipzig drew 3-3 at Dortmund Tuesday.

Dortmund also have 30, and Schalke 29 after a 1-1 draw at Wolfsburg.

Elsewhere, visiting Hertha Berlin surprised Bayer Leverkusen 1-0 on Wednesday for a second straight victory under new coach Juergen Klinsmann and Cologne came from 2-0 down to win 4-2 at Eintracht Frankfurt to leave the danger zone.

Munich started in Freiburg as dominant as in their 6-1 demolition of Werder Bremen on Saturday, with Philippe Coutinho almost scoring in the opening minute and Thomas Muller denied by the post five minutes later.

Lewandowski then put them in front off Alphonso Davies' sharp cross from the left in the 16th but they allowed Freiburg back into the game.

The hosts got an equaliser in the 59th from Grifo's drop volley into the left corner off Janik Haberer, and they also had chances to take the lead.

But with time running out the unheralded Zirkzee slotted home and Gnabry then wrapped up matters for a lucky victory.

Coming off a late defeat in Wolfsburg, Gladbach had plenty of trouble against Paderborn before taking the lead seconds after the restart, Patrick Herrmann stealing the ball and Alessane Plea firing home from some 12 metres.

Captain Lars Stindl then grabbed his first goal of the season after a lengthy injury lay-off from the spot in the 67th.

Australian Associated Press