Paul Mueller, the orchestra's chief executive since 2002, also extended his contract, through the 2010-11 season.
"In the four-year period in which Jonathan Nott and Paul Mueller have been at its helm, the Bamberg Symphony Orchestra has experienced a major overhaul which has vastly strengthened its position both financially and artistically," a statement from the orchestra read.
Under Nott's leadership, the Bamberg Symphony traveled to the Edinburgh Festival in 2003 and made its New York debut at Lincoln Center in 2005. This spring, he will take the orchestra on a tour of Japan.
The 43-year-old Nott, who is British-born, has also established a reputation as a leading guest conductor, especially of contemporary music. He led the New York Philharmonic for the first time last month, conducting John Corigliano's Red Violin Concerto.
Formerly the principal conductor of Paris's Ensemble Intercomtemporain, Nott is now the new-music group's principal guest conductor.