The senior who scored the No. 7 Trojans' go-ahead touchdown against Ohio State two weeks ago was bench-pressing when the bar slipped from his right hand and fell onto his throat.
Johnson was in critical but stable condition late Monday night after more than seven hours of surgery, said Katreena Salgado, a spokeswoman for California Hospital Medical Center.
He was treated for crushing injuries to his neck as well as severe injuries to his larynx, said the hospital's trauma medical director, Dr. Gudata Hinika. Stan Johnson, the player's father, told ESPN's Shelley Smith that his son needed a tracheotomy to enable him to breathe.
According to the Los Angeles Times, a source close to the family said surgeons worked to realign Johnson's larynx in hopes he will be able to use his voice.
It's unlikely Johnson will be able to play again this season, but his prognosis is good and doctors expect him to make a full recovery, Hinika said in a statement released by the hospital.
"It hit him with a lot of force, and it hurt him," coach Pete Carroll said after the Trojans' brief practice Monday night but before the surgery was finished. "No broken bones as far as I understand, but he's got some damage in there somewhere, and they're working it out, trying to figure out what it is. ... It is serious. He did get hurt, so we don't know exactly what it is, and they're not going to know until they go through the surgery."
Immediately after the accident, Johnson was coughing up blood, a source close to the USC football program told ESPN's Smith.
Carroll said Johnson "was OK," but couldn't speak, when he left the weight room for California Hospital Medical Center. Johnson's family and friends gathered at the hospital on Monday to await word on his surgery.
Carroll tweeted his concern later Monday evening. "Please keep Stafon Johnson in your thoughts and prayers ... still in throat surgery after weights accident this AM," it read.
Earlier, Carroll said that weight room incidents are not entirely uncommon.
"That happens sometimes when you're doing bench presses, but this one just hit him wrong," Carroll said. "You can miss the rack or something. This was right at the end of his set, and he wasn't putting the bar down on the rack yet."
An assistant strength and conditioning coach was standing over Johnson at the time of the accident.
"I've seen players have the bar slip and fall onto their chest, but never in my 25 years of coaching have I heard of someone dropping a bar on their throat," said head strength and conditioning coach Chris Carlisle, who was standing 10 feet away at the time of the accident. "We're fortunate he was being spotted."
Johnson, a 5-foot-11, 210-pound senior from Compton, Calif., is the Trojans' second-leading rusher and goal-line specialist. He's rushed 32 times for 157 yards this year and leads the team with five touchdowns. He entered the season with 1,395 rushing yards and 14 touchdowns.
Information from ESPN.com Pac-10 writer Ted Miller and The Associated Press was used in this report.