Frankfurt:Defending champion Nuremberg was eliminated by second-division Carl Zeiss Jena in the second round of the German Cup on Wednesday.
Last season's runner-up Stuttgart squeezed through on a goal by Mario Gomez late in extra time against Paderborn, another second-division team.
Luca Toni scored two goals in the second half to help Bundesliga leader Bayern Munich beat old rival Borussia Moenchengladbach, which now tops the second division, 3-1.
Toni opened the scoring in the 47th minute, capitalizing on a goalkeeping mistake and heading in at the far post off a cross from Lukas Podolski. The Italian doubled the lead 10 minutes later with a shot from the edge of the penalty area.
But the visitors stunned Bayern in the 70th minute when Marcel Ndjeng scored from more than 30 meters, driving the ball over Bayern's goalkeeper Michael Rensing.
Rensing, who was again playing for Oliver Kahn, still recovering from elbow surgery. He made several good saves earlier but appeared overmatched on the long-range shot.
Miroslav Klose secured the win in the 83rd, a few minutes after replacing Toni.
In Jena, Nuremberg led twice but could not protect the lead and conceded a goal in the 114th minute to make it 2-2, after 1-1 in regulation time. Jena won the penalty shootout 5-4 to advance.
Gomez scored two minutes before the end of extra time to give Stuttgart a 3-2 win against the worst team in the second division, after Stuttgart had squandered a 2-0 lead.
Werder Bremen beat Duisburg 4-0 on goals from Tim Borowski, Hugo Almeida, Markus Rosenberg and John Mosquera.
Borussia Dortmund rallied to beat last year's semifinalist Eintracht Frankfurt 2-1, getting goals from Markus Brzenska and Mladen Petric after the visitors led on a goal by Ioannis Amanatidis.
Hamburger SV beat second-division Freiburg 3-1 on goals by Piotr Trochowski, Ivica Olic, and captain Rafael van der Vaart, who converted a penalty in the final minute.