The American completed the stage from Bad Tolz to Seefeld in Austria ahead of Andrei Kaschechkin of Kazajhstan and Italian Marzio Bruseghin.

Fourth home Jens Voigt of Germany took over the overall leader's jersey from compatriot Erik Zabel.

The riders threatened not to start because of the heavy rain and forced the organisers to cut the route by 30km, losing a major climb.

"You have to think of the safety of the riders. The conditions were unacceptable," said Zabel.

But the abrieviated stage may have cost him the leader's jersey as Voigt admitted that the changes had helped him.

"I benefited from the shortened course," said the 34-year-old Voigt. "The big mountain was removed from the run and that helped me."

Leipheimer's win moved him up to fourth in the standings.

Tour of Germany stage five result:
1. Levi Leipheimer (US/Gerolsteiner) 3hrs 44:20
2. Andrei Kascheckin (Kazakhistan/Astana) +2",
3. Marzio Bruseghin (Italy/Lampre) same time
4. Jens Voigt (Germany/Team CSC) same time
5. Leonardo Piepoli (Italy/Saunier Duval) same time

Overall standings:
1. Jens Voigt (Germany/Team CSC) 22:27:51"
2. Vladimir Gusev (Russia/Discovery Channel) +3"
3. Marzio Bruseghin (Italy/Lampre) +13"
4. Levi Leipheimer (US/Gerolsteiner) +18"
5. Inigo Cuesta (Spain/Team CSC) +25"