Salt Lake County District Attorney Sim Gill announced the charges, saying he will seek to try the teen as an adult.
A homicide by assault charge is less serious than manslaughter. It carries up to five years in prison for adults, but penalties can be less for juveniles.
Gill said it became clear in looking at the facts that the teenager's actions didn't warrant murder or manslaughter.
"We did not believe we could demonstrate the premeditation or intent to justify those charges," Gill told The Associated Press on Wednesday. "Those other charges require another type of mental state. We did not believe that type of mental state was present."
The 17-year-old has been in juvenile detention since April 27 when the incident occurred at a recreational-league soccer match in a Salt Lake City suburb.
Authorities say the teenager was playing goalie when 46-year-old Ricardo Portillo called a penalty on him for pushing an opposing player. The teenager began arguing with Portillo and then struck him in the head.
Charging documents show witnesses say the teenager threw one punch, hitting him in the rear jaw area with a closed fist. Another witness said Portillo was writing notes on his notepad when he was hit.
Portillo was taken to the hospital in fair condition. Hours later, he went into a coma. He never regained consciousness and died Saturday.
Police say hospital staff told them Portillo had hemorrhaging and a traumatic brain injury.
The fact that the teenager is five months away from turning 18, combined with the seriousness of what happened, led Gill to push to have him tried as an adult. A juvenile court judge will ultimately rule on that request.
The chance of the teen's rehabilitation is minimal, prosecutors said in court documents.
League officials say they hadn't had any problems with the teenager prior to this incident.
Funeral services are being held Wednesday in Salt Lake City for Portillo, who leaves behind three daughters and four grandchildren.
A wake is scheduled to run from 1 to 7 p.m., followed by a religious service. Both are open to the public.
After the funeral, Portillo's remains will be returned to his hometown of Guadalajara, Mexico. He moved to Utah from there 17 years ago.
Family members said Portillo loved soccer, and had been working as a referee in different leagues for eight years. His oldest daughter, Johana Portillo, said he had been attacked before by players, even having his legs and ribs broken. Though his daughters begged him to quit, he said he couldn't give up his passion.
Portillo was a longtime referee, be he was not licensed by the Utah Soccer Referee Committee.
The incident occurred in a game held by La Liga Continental de Futbol, an unaffiliated soccer league created in 2009. The league holds games for children ages 4 to 17 each Saturday at a junior high school field in Taylorsville.
The league president, Mario Vasquez, said earlier this week that the league will hold an adult, co-ed soccer tournament in Portillo's honor May 25-26. The funds will go to his family.