Bieber, 20, paid more than USD 10,700 last week for the March 2013 incident in which he brought his Capuchin monkey Mally into the country without the necessary paperwork or vaccinations, reported the New York Post.
The money will be used to cover the monkey's cost of living at the shelter for the past 17 months, as well as his import, according to a spokesperson with the German Federal Nature Conservation Agency.
Bieber received Mally as a gift from music producer Jamal Mally Mal Rashid for his 19th birthday.
He found himself in hot water when he treated the pampered pet to a lavish trip on his private jet to Germany, a stop on his concert tour.
When Bieber landed, customs officers swarmed his plane, seized the monkey and handed it over to an animal clinic.
Instead of providing the proper paperwork to keep ownership of Mally, the Canadian singer opted to abandon the monkey.
Mally is now living at a zoo in north Germany.