Thiago Alcantara scored the winning penalty as Bayern Munich edged out Bayern Leverkusen to reach the German Cup semi-final - but was lucky to still be on the pitch . As the Spaniard challenged for the ball , he followed through with a kick into the chest of Leverkusen 's Stefan Kiessling . With the match deadlocked at 0-0 at the end of extra time , Thiago then converted the decisive penalty in the shootout after Bayern goalkeeper Manuel Neuer had saved Josip Drmic 's effort . Scroll down for video . Thiago Alcantara challenged for the ball but followed through with a nasty kick into Stefan Kiessling 's chest . Thiago 's kick went unpunished and he later helped his side through to the semi finals of the German Cup . Kiessling was taken off shortly after the incident as the cup tie headed for half time . Thiago peels away after scoring the winning penalty in the shootout against Bayer Leverkusen . Manuel Neuer makes a save from the spot as German Cup holders Bayern Munich progress . Neuer gets down well to deny Bayer Leverkusen ace Josip Drmic from the spot as the game went to penalties . Neuer and Thiago Alcantara acknowledge each others ' contribution as they progress to the semi-finals . The Bayern Munich squad run towards Neuer following Thiago Alcantara 's winning penalty in Leverkusen . Bayern 's goalkeeper Neuer makes a save after a shot by Bayer Leverkusen 's Karim Bellarabi . 'Penalties are always a matter of luck , ' said Bayern forward Thomas Muller , who converted from the spot . 'This match cost us a lot of nerves . ' The victory kept Pep Guardiola 's team on course for a repeat of the 2013 treble . His team is the far away leader in the Bundesliga and is also in the quarter-finals of the Champions League . Guardiola watched the shootout calmly from a chair on the sidelines . Both teams had chances to settle the issue earlier , with Mueller coming close late in the first half and Neuer foiling Karim Bellarabi after the break . Neuer gets down well to deny Bellarabi during their German cup match in western Germany . Wendell challenges Mario Gotze during the quarter-final German Cup game in Leverkusen . Bayern Munich 's midfielder Sebastian Rode vies for the ball against Spahic on Wednesday night . At the other end , Bernd Leno parried Robert Lewandowski 's effort , before Neuer denied Bellarabi once again in a pulsating match . Bayern 's Rafinha made a vital lunging clearance to prevent Julian Brandt from getting off a clean shot as the 90 minutes came to an end . Mario Gotze wasted Bayern 's best chance in the 98th , missing the target from close range while unchallenged at the far post . Bayern played without the injured Arjen Robben , Franck Ribery and Bastian Schweinsteiger . Bayern 's Dante from and Leverkusen 's Stefan Kiessling challenge for the ball during the German cup game . Spahic puts his head where it hurts as Thomas Muller goes in with a raised boot in Leverkusen . Bayern 's head coach Pep Guardiola directs his players during their German cup game on Wednesday night . Leverkusen 's Bellarabi and Bayern 's Gotze challenges for the ball during a German cup match .
It took penalties , but holders Bayern Munich progressed to the semi-finals . Manuel Neuer and AlcantaraThiago Alcantara starred as they won the shootout . Thiago Alcantara was lucky to still be on the pitch after making a nasty challenge . Robert Lewandowski also had a legitimate goal mistakenly ruled out .