BERLIN, Feb 26 (Reuters) - Bundesliga champions VfB Stuttgart were knocked out of the German Cup by second division strugglers Carl Zeiss Jena on Tuesday, losing their quarter-final on penalties after extra time ended at 2-2. In Tuesday's other quarter-final, Borussia Dortmund eased past second division 1899 Hoffenheim 3-1. Stuttgart looked to be heading for victory at 2-1 up in the second period of extra time but Robert Mueller took advantage of a mistake by goalkeeper Sven Ulreich in the first minute of injury time and stroked the ball into the empty net. Antonio da Silva missed the decisive penalty, firing Stuttgart's fourth over the bar, and Torsten Ziegner then stepped up to make it 5-4 to the eastern German club and book their place in the semi-finals. Striker Tobias Werner had given Jena a surprise lead in the 32nd minute, latching on to a long cross from the right and nodding past Ulreich. Faced with some resolute defending, the Bundesliga champions had to wait until the 81st minute before Mario Gomez levelled. The tall striker then netted again with a header in the fourth minute of extra time before Jena's last-gasp equaliser and the penalty drama. In Dortmund, Giovanni Federico put the home side ahead after 20 minutes. The Italian midfielder struck from 20 metres after good work from Tinga and the Brazilian extended Dortmund's lead three minutes later, nodding in from close range. Hoffenheim's Francisco Copado scored from the penalty spot just before halftime to make it 2-1, before Mladen Petric made the match safe for Dortmund in the 54th minute. In Wednesday's two quarter-finals, Bundesliga leaders Bayern Munich play city rivals TSV 1860 Munich and VfL Wolfsburg take on Hamburg.