The 39-year-old India-born celebrity fashion designer was arrested in 2007 in California on charges that he preyed upon seven young aspiring models, some as young as 14 and sexually assaulted them.
He is currently serving 59 years to life in prison in California.
Alexander had pleaded guilty in February to one count of criminal sexual act in Manhattan Supreme Court.
The prison time of five years in New York amounts to time served in California, which means no additional years will be added to Alexander's California sentence of 59 years.
Judge Cassandra Mullen announced the prison term for Alexander who said in court, "I would like to thank everyone for being here."
Alexander's sister Sanjana Jon was among several supporters who were present in court for the sentencing and held banners that read 'Free Anand Jon'.
In a plea deal reached with federal prosecutors, Alexander had pleaded guilty to one count of criminal sexual act against one aspiring female model.
In turn, Manhattan prosecutors dropped almost their entire case against him.
He had initially been charged with preying on a dozen women in a 49-count indictment in New York.
Assistant District Attorney Maxine Rosenthal had said the plea deal was accepted "to spare the victims from having to testify at multiple proceedings" and in consideration of Alexander's lengthy sentence in California.
Rosenthal said Alexander is facing similar charges in Texas.
The Kerala-born fashion designer had launched a fashion line in 1999 and was featured on 'America's Next Top Model' working with celebrities such as socialite Paris Hilton.
His designs have been worn by media mogul Oprah Winfrey and singer Janet Jackson.
His attorney said Alexander admitted to the crime so he could get evidence and materials from New York prosecutors needed to "effectively overturn his California conviction".
He said some of the materials turned over by Manhattan prosecutors as part of the pre-trial process would be crucial as Alexander continues to work on his California appeal.
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