Francis Wayne Alexander’s remains were among those found in the crawl space of Gacy’s Chicago-area home in 1978.
Cook County Sheriff Tom Dart ordered eight unidentified victims’ bodies to be exhumed in 2011 in an effort to identify them through DNA testing.
Alexander is the third Gacy victim to be identified in the last decade.
He would have been 21 or 22 when Gacy killed him between 1976 and 1977, Mr Dart’s office said.
Gacy was convicted of killing 33 young men between 1972 and 1978 and burying them on his property. He was executed in 1994.
He often lured young men to his home for sex by pretending to be a police officer or promising them construction work.
In reopening the investigation, Sheriff Dart asked families of youngsters who had vanished between 1970 and Gacy’s 1978 arrest to submit saliva samples to compare DNA with the eight victims who were buried without being identified.
Months later, William George Bundy, a 19-year-old construction worker, was identified as a Gacy victim.
In 2017, James Byron Haakenson – a missing teenager from Minnesota – was named as another victim.
Investigators matched DNA samples from Mr Alexander’s mother and half-brother to his remains.
Alexander’s sister, Carolyn Sanders, thanked the sheriff’s office for giving the family “closure”.
“It is hard, even 45 years later, to know the fate of our beloved Wayne. He was killed at the hands of a vile and evil man,” Ms Sanders said.
“We can now lay to rest what happened and move forward by honouring Wayne.”
Authorities say they are unsure how Mr Alexander’s crossed paths with Gacy, one of America’s most infamous serial killers.
He had moved to Chicago, where he was married for around three months before divorcing in 1975.
In January 1976, he received a traffic ticket in Chicago. After this, officers found no record of him being alive.
Mr Alexander “lived in an area that was frequented by Gacy and where other identified victims had previously lived”, the sheriff’s office said.
Police say their efforts to identify the other remains are ongoing.