Pierre-Emerick Aubameyang scored his 21st league goal in Borussia Dortmund's controversial 1-0 win at Bayer Leverkusen on Sunday after the referee made Bundesliga history by briefly stopping play.

Confusion reigned for around nine second-half minutes at Leverkusen's BayArena when Bayer coach Roger Schmidt refused to be sent to the stands by match official Felix Zwayer amidst tense scenes.

The 48-year-old Schmidt was furious that Dortmund were allowed to take a free kick in the build up to Aubameyang's 64th-minute winner and stood his ground.

The controversy was triggered when Leverkusen striker Stefan Kiessling pushed over Dortmund's Sven Bender in the Borussia half.

Zwayer awarded a free kick, which Matthias Ginter quickly took.

The move swept down field and Germany defender Erik Durm's pass pulled the Leverkusen defence to create space for Aubameyang to hit the winner.

The Leverkusen team, with Kiessling and Schmidt at the forefront, furiously protested that the game should have been stopped for the free-kick to be taken.

When Schmidt refused Zwayer's demand that he went to the stands, the Berlin official marched the teams off until the Bayer coach took a seat in the grandstands.

It was the first time in Bundesliga history that a game has been stopped under such circumstances.

When play resumed, Leverkusen's star striker Javier Hernandez wasted a golden chance in added time to equalise by firing over the bar with the goal at his mercy.

Dortmund's controversial victory leaves them eight ponts behind runaway league leaders Bayern Munich who beat Darmstadt 3-1 at home on Saturday.

Thomas Mueller netted twice to dig Bayern out of trouble in their last match before their Champions League clash at Juventus before Robert Lewandowski added their third goal.

Against the run of play, Pep Guardiola's Bayern went behind when Darmstadt's Munich-born striker Sandro Wagner headed home midway through the first half.

It was only the fifth time this season Bayern had gone behind.

But using their 81 percent possession to fire in a total of 36 shots on goal to Darmstadt's six, Guardiola's side roared back to claim their 19th win in 22 league games this season.

Bayern were back level four minutes into the second half when Mueller slammed his shot into the right-hand corner.

He added a superb second -- his 17th league goal of the season -- by chesting down Arturo Vidal's cross and hitting a bicycle kick into Darmstadt's net on 71 minutes.

Lewandowski added the third on 84 minutes when he converted Franck Ribery's low cross after the Frenchman came off the bench for only his third appearance of the season.

It was Lewandowski's 22nd goal of the season in 21 league games to leave him as the league's top scorer.

Elsewhere, fresh from their 3-2 Champions League win at Gent in midweek, Wolfsburg picked up a point in the capital with a 1-1 draw at Hertha Berlin.

Wolves took the lead at the Olympic Stadium when Marcel Schaefer converted Vieirinha's cross on 53 minutes, but Salomon Kalou on the hour mark.

Julian Nagelsmann, the Bundesliga's youngest ever coach at 28, steered Hoffenheim to only their third win of the season on just his second match in charge with a 3-2 victory at home to Mainz.

Hoffenheim remain 17th, but are now only three points from safety after Werder Bremen, who are 16th, lost 2-0 at Ingolstadt.

Cologne fans protested about the price of away tickets at Borussia Moenchengladbach as the hosts sealed a 1-0 win thanks to Mahmoud Dahoud's first-half goal.