The incident occurred on Flight 8623, which departed Toronto for Atlanta at 2:20 p.m. ET on Friday and landed just after 4:30 p.m.
Oliver Minatel, a 22-year-old Fury forward, said he was sleeping when a man jumped on him and choked him with a headphone cord.
"He just jumped on me," Minatel told CNN reporter Paula Newton, who was also on the plane and recorded the aftermath of the incident. During her interview with Minatel, other passengers could be seen in the background repeatedly telling the man to remain seated and put his seatbelt on.
Members of the soccer team told CBC News that before boarding the plane, a man was pulled aside to be questioned by security officials.
That same man was later seated on the plane just behind Minatel, according to coach Marc Dos Santos.
About 10 minutes before the plane began its descent into Atlanta, Dos Santos said he and other passengers saw the man attempt to use the cord of his headphones to choke Minatel.
Another passenger quickly intervened to stop the attack, Dos Santos said.
"Somebody tried to choke one of our players, out of the blue, and it wasn't a fun moment … and I think some of our guys are in shock, but now everything's back to order," Dos Santos told CBC News in a Skype interview from the airport in Atlanta on Friday evening.
Minatel was shaken up by the incident but not injured.
'It was like a movie,' coach says
The Fury flew to Atlanta to play their second away game of the season against the Atlanta Silverbacks. The North American Soccer League game is set to go ahead on Saturday as planned.
"He's good now. We went through everything we had to go through with him with the local police and even the FBI. It was like a movie, you know?" Dos Santos said.
"It was a little bit of a scary moment. We'll eat well tonight, we'll try to sleep well and tomorrow we have a game to play and hopefully everything's going to go well."
Atlanta police assisted the FBI in removing the suspect from the plane once it landed, Atlanta police said in an email to CBC News on Friday evening.
The suspect was then taken to hospital by Atlanta police for medical and mental evaluation, according to an emailed statement from the FBI.
"While there are currently no federal charges pending, the facts of the matter are being relayed to the U.S. Attorney's Office in Atlanta," the FBI wrote.
Air Canada Jazz would not provide details of the incident, citing privacy concerns, but a spokesperson did say the crew asked police to meet the plane at the airport.
"The safety of our passengers and crew are our top priority and our crew members are well trained to handle challenging situations. We have a zero tolerance policy with respect to unruly behaviour," the spokesperson wrote in an email.