The withdrawal of the soldiers must be completed by the end of June.
The operation has been ongoing since 2007 and at most 16,000 UN soldiers have been on site at the same time.
Amnesty International criticizes the decision and wants the effort to continue.
"The UN Security Council must extend the mandate of the peacekeeping forces by at least six months, due to the government's failure to protect civilians," the organization said in a statement earlier in December.
According to the UN, the conflict in Darfur has claimed almost 300,000 lives. 2.5 million people are currently fleeing their homes as a result of the unrest.