The council unanimously adopted a resolution that will end the mission known as MINUSTAH by October 15.
The decision provided a boost to the new US administration's hopes of cutting back its multi-billion dollar financial contribution to UN peacekeeping.
US Ambassador Nikki Haley has launched a review of all peacekeeping missions to find ways of cutting back costs and improving the operations, which have been plagued with sexual abuse and corruption scandals.
After the vote, Haley spoke out against sexual abuse by UN peacekeepers, saying children in Haiti will continue to face a "nightmare" after the troops are gone.
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The council agreed that the 2,370 soldiers serving in MINUSTAH will be gradually withdrawn over six months to make way for the new United Nations Mission for Justice Support in Haiti (MINUJUSTH).
That mission will have 1,275 police, which will also be drawn down over two years as the police force is built up in the poor Caribbean country.
MINUSTAH was deployed in 2004 after the departure of president Jean-Bertrand Aristide to help stem political violence but it has not endeared itself to Haitians.
An outbreak of cholera in 2010 was introduced by Nepalese UN peacekeepers serving in the mission. More than 9,000 Haitians died in the epidemic.
She cited the example of a sex ring allegedly run by Sri Lankan peacekeepers in Haiti -- they reportedly lured hungry teenage boys and girls by offering them snacks and cookies. Dozens of peacekeepers were sent home over the claims.
"The children were passed from soldier to soldier," Haley told the council.
"Countries that refuse to hold their soldiers accountable must recognise that this either stops, or their troops will go home and their financial compensation will end," she said.