Chicago head coach Gregg Berhalter confirmed the 20-year-old sustained the injury during a training session, with the centre-back expected to miss several weeks and potentially longer depending on his recovery.
"It's not good," Berhalter said after Chicago's 3-1 defeat to New York City FC. "He's going to be out for a while. He took a shot in training, hit the ground a little bit, scuffed the ground, and ended up tearing his thigh.
"And it's serious. He won't be back for a good amount of time."
The injury has already ruled Mbokazi out of this week's MLS All-Star Game, where he had earned the most fan votes of any player, including Lionel Messi, after an outstanding debut season in the United States and an impressive FIFA World Cup campaign with South Africa.
Chicago have placed the former Orlando Pirates defender on the six-week injured list, although Berhalter admitted the lay-off could extend beyond that. Mbokazi is set to miss at least six MLS fixtures, the club's Leagues Cup campaign against Necaxa, Santos and Cruz Azul, and is unlikely to return before mid-September.
His absence also leaves him in doubt for Bafana Bafana's opening 2027 Africa Cup of Nations qualifiers against Guinea and Eritrea in late September.
Berhalter acknowledged Mbokazi's importance to the Fire, who have already been without him for defeats to Inter Miami and New York City following the MLS restart after the World Cup.
"It is a miss," Berhalter said. "We feel like we have good centre-backs there anyway, but because he's a top centre-back, we're going to be missing him for a while. So we've got to get used to the new normal."
The injury has left Chicago short of options in central defence, with only three senior centre-backs currently available. Berhalter admitted the club is considering strengthening the position or recalling highly rated youngster Christopher Cupps from international duty with the United States Under-20 side.
"We don't have an answer for it right now," he said. "It is something that we're considering. We have a busy schedule. We need everyone on deck. There's Cupps, who's away on international duty, so maybe we bring him back. But it's something we're considering for sure."
Mbokazi's absence comes at a frustrating time after his stock rose sharply over the past two months. The 20-year-old impressed throughout South Africa's World Cup campaign before continuing his strong form in MLS, attracting widespread praise and reportedly putting himself on the radar of clubs ahead of the transfer window.
Fellow South African Puso Dithejane admitted losing Mbokazi is a setback but backed the squad to cope.
"Losing Mbokazi, an important player in our team, is a bad thing," Dithejane said. "We have players who can do what he's been doing."
Berhalter also singled out Dithejane for praise after the winger continued his impressive pre-season form by scoring against Inter Miami.
"He's been the star of this new preseason that we've had," Berhalter said. "He scored against Minnesota, he scored against Columbus, and now he scores again against Miami.
"He's coming on, pushing for minutes. You can see how dangerous he is, and he has a bright future."