Brisbane trailed 12-0 at the time of Yow Yeh's injury, but piled on four unanswered tries to surge to the win in front of 15,599 fans.
Substitute Matt Gillett and fullback Josh Hoffman started the comeback with tries either side of halftime.
And winger Gerard Beale added the finishing touches, crossing in the 70th and 74th minutes to stun the Rabbitohs.
Earlier, South Sydney star Greg Inglis continued his inspiring form at fullback as he set up his side's opening two tries.
Winger Andrew Everingham was the beneficiary on both occasions, with the highlight being Inglis' piercing run to set up the first try.
The Rabbitohs' defence was rock solid in the opening 35 minutes, but a fumble from Farrell opened the door for Brisbane to open their account in the 39th minute.
Farrell's spill of a high ball gifted Gillett an easy try, and when Hoffman crossed in the 53rd minute, the Rabbitohs were looking nervous.
Beale's double strike in the final 10 minutes proved to be the killer blow.
Peter Wallace's grubber kick set up Beale's first, and the winger was on hand again in the 74th minute when a quick series of passes allowed him to sneak across in the corner.
The Rabbitohs' third loss of the season leaves them behind the eight-ball early on, while Brisbane (3-1) are in a solid position.
Brisbane coach Anthony Griffin said Yow Yeh had suffered a suspected broken ankle.
Thaiday said he and Hodges tried to get the medical staff to give Yow Yeh pain relief as quickly as possible after the incident occurred.
"He's laying there with his bone sticking outside of his boot," Thaiday said.
"He was in a lot of pain there.
"Hodgo and I were just trying to encourage him as much as we could.
"The first thing that goes through your head when you get injured is your footy, and then your career and season.
"He was asking questions along the lines of those things.
"We were just reassuring him and making sure that he knew that we were there for him and supporting him."
South Sydney coach Michael Maguire rued his team's sloppy performance once they had established a 12-0 lead.
"I think in that first half we had control and unfortunately we went away from our plan ... and allowed the Broncos to get back into the game," Maguire said.
"An example of that was the try before the end of the half. Unfortunately there was an error and they got a try out of that."
- AAP