Rafael Toirac-Aguilera, 33, made a brief court appearance Thursday morning after he was indicted Wednesday on first-degree murder charges.
Toirac-Aguilera was extradicted from New Jersey Wednesday and is in custody at the Turner Guilford Knight Correctional Center.
Toirac-Aguilera is accused of the execution-style murder of Yee on July 10, 2009, at the Hurricane Cove Marina.
Retired after 25 years on the force, Yee, 61, was working as a security guard at the Marina at 1884 NW North River Drive.
He was found with multiple gun shot wounds to the back of his head and died a short time later at Jackson Memorial Hospital.
In February, it was revealed that a New Jersey man suspected in the Yee murder had been arrested on unrelated charges on a sealed Grand Jury Indictment from Miami-Dade.
An arrest warrant released Thursday said Toirac-Aguilera became a suspect when his DNA and a fingerprint were recovered from an orange juice bottle left at the scene of the murder.
Police believe the orange juice bottle was used as a makeshift silencer on the weapon that killed Yee.
Additionally, Toirac-Aguilera's girlfriend told police they the two had driven from New Jersey to Miami to visit friends in a silver Toyota Corolla in July 2009, and that Toirac-Aguilera was gone for hours on the day of the Yee murder.
When detectives questioned Toirac-Aguilera about where he was on July 10, he said he was in New Jersey working at a body shop.
Police said Yee's killer left the marina in a Silver Corolla.