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 Thiago Alcantara starred as they won the shootout.
Alcantara was lucky to still be on the pitch after making a nasty challenge.
Robert Lewandowski also had a legitimate goal mistakenly ruled out.