Panthers fullback Matt Moylan may have been playing with a broken hand and dislocated fingers but he still grasped an opportunity to snatch the result, kicking a 76th minute field goal that set up Penrith's 5-4 lead.
Moylan racked up all of Penrith's points, sinking penalties either side of halftime including a 56th minute kick that locked up the scores at 4-4 after a Josh McGuire high shot.
Brisbane had their chances before Hunt's heroics - returning back-rower Alex Glenn was held up in the 65th minute and Jack Reed lost the ball over the line four minutes later.
The Broncos appeared to be sparked into action in the 60th minute when Panthers reserve Tyrone Peachey was placed on report for a lifting tackle on Adam Blair that almost sparked a melee.
The ladder leading Broncos have now won seven of their past eight games.
Penrith fought hard despite a long casualty list even after welcoming back Jamie Soward (back) and Elijah Taylor (knee).
Brisbane led 4-2 at halftime after Jordan Kahu broke the deadlock in the 36th minute when Hunt and Anthony Milford combined to send the winger over down the left sideline.
Penrith coach Ivan Cleary was clearly baffled when Moylan was penalised after appearing to clean up a Boyd grubber late in the second half.
Moylan gathered the bouncing ball outside the playing field well behind the in-goal but was penalised for not allowing the ball to bounce, therefore ensuring it had gone dead.
It gave Brisbane a repeat set from a goal-line drop out as they started to get a late roll on.
"It was one of the most ridiculous things I have seen in football," Cleary said of the official's call.
"There's no common sense at all.
"I am not sure of the rule but for them (officials) to highlight it like that, it's a massive change in a very tight game."
Broncos coach Wayne Bennett said he was aware of the rule after being caught out by it last season while coaching Newcastle.
"They came to spoil, not play," he said of Penrith.
"It's pretty unique what they did. I am pleased we hung on for as long as we did.
"It came down to one big play (by Hunt)."
- AAP