Winger Bryson Goodwin attempted a quick tap only to be stripped himself illegally.
Referee Gavin Badger blew the penalty again and South Sydney quickly regained their cool before Adam Reynolds potted over the 78th minute match-winning goal.
Remarkably a Greg Inglis-inspired South Sydney led Brisbane (both 4-4 records) 14-0 after just 15 minutes only for the hosts to snatch a two-point halftime lead.
Inglis set up hooker Apisai Koroisau (7th minute) and debutant Alex Johnston - replacing winger Nathan Merritt - in the 11th.
Then Inglis swooped on a Ben Barba chip to run 89m and swat away seven defenders to file an early nomination for try of the season.
It could have been worse - the video referee denied centre Dylan Walker a 25th minute try after replays showed backrower Ben Te'o knocked on Reynolds' grubber in the lead-up.
A minute later Inglis showed he was human when he knocked on a Dale Copley grubber close to his line and Andrew McCullough (26th) scored.
Brisbane hit the lead 16-14 when they capitalised on a remarkable 10 straight sets as winger Lachlan Maranta (30th) and lock Matt Gillett (35th) crossed.
The Broncos were up 22-14 when McCullough (43rd) burrowed over from dummy half but South Sydney hit back through a barnstorming George Burgess (52nd) to make it 22-20 to the hosts.
Jack Reed pounced on a Hunt grubber but Corey Parker missed the conversion to make it 26-20 to leave the door open for South Sydney.
South Sydney coach Michael Maguire tipped his hat to his side for winning the "dog fight" after being on the wrong side of last round's similarly controversial loss to the Bulldogs.
"We obviously learned some lessons from last weekend," he said.
Asked about the final two penalties where Burgess was stripped and a Broncos player was ruled off-side raking the ball from Goodwin, Maguire said: "I was pretty pleased they went our way."
Asked about the obstruction rule, Maguire said: "The ruling is pretty straight forward but it is a bit hard to tell sometimes."
Maguire revealed pivot John Sutton (quad) should not have played after suffering a training injury.
Broncos coach Anthony Griffin blamed his side's composure rather than the officials for the loss.
"We are finding ways to lose in ridiculous ways," he said.
"I am not sad. I am not reliant on their calls being right or not.
"That's the theatre of the game."
But asked if he understood the obstruction rule, Griffin said: "Do you? "No, I don't.
"But their (officials') calls are their calls. We could have put the game to bed but we didn't."
- AAP