Biletnikoff was the daughter of former Oakland Raiders wide receiver and Pro Football Hall of Fame member Fred Biletnikoff.
Chief Deputy San Mateo County District Attorney Stephen Wagstaffe said today that prosecutors will go ahead with a retrial.
"The evidence against him was strong then and it is strong now," he said.
In his first trial, Ali was found guilty in San Mateo County Superior Court in 2001 of first-degree murder and sentenced to 55 years to life in prison.
Ali met Biletnikoff through a San Mateo County drug treatment program where they were both working as counselors after having recovered from drug addictions.
Biletnikoff's body was found on Feb. 15, 1999, on the campus of Canada College near Redwood City. Ali was arrested the next day in San Diego.
He admitted to strangling her during an argument over his relapse into alcohol and drug use, but contended the crime should be considered manslaughter rather than murder.
Last year, the 9th U.S. Circuit Court of Appeals in San Francisco overturned the conviction, saying that prosecutors had dismissed at least one and possibly two black jury candidates from the jury pool for improper reasons of racial discrimination.
In Monday's order, the Supreme Court turned down state prosecutors' appeal of that ruling.
Ali, who came to the United States from Fiji as a teenager, contended he acted in the heat of passion during the argument with Biletnikoff because he feared being deported to Fiji as a result of the relapse. A heat-of-passion finding would make the crime manslaughter rather than murder.
His lawyer in the appeal, A.J. Kutchins, was not immediately available for comment.