A distraught Papenhuyzen was carted off Suncorp Stadium in agony after his leg was caught while making a tackle with seven minutes to play in the Storm's 26-0 qualifying-final defeat to Brisbane on Friday.
He was sent straight to hospital with a suspected broken ankle and had surgery on Saturday morning.
Storm general manager of football Frank Ponissi on Saturday clarified it was "definitely not a compound fracture" - meaning the bone had not pierced the skin - and that the flyer was aiming to return to training "in the new year".
The 2020 Clive Churchill Medal and premiership-winning fullback shattered his right kneecap into 10 pieces in July of last year.
Friday's game was just his third NRL appearance since his August return against Gold Coast ended a 405-day NRL absence.
The gruesome nature of his latest setback prompted fears of another long lay-off, but Ponissi remained optimistic for the 25-year-old.
"Scans overnight suggest that it may not be as serious as first feared," he told AAP.
In a later update on the club website Ponissi said "surgery went well".
"This is just another challenge that he will take on with both hands," he said.
"At this stage, we expect him to be back training in the new year but for now we're focused on ensuring he is getting the right care."
From his hospital bed, Papenhuyzen posted a photo to social media giving the thumbs up with the caption: "We go again. Love ya".
The late mishap overshadowed Brisbane's dominant win that broke a losing streak against the Storm at the venue stretching back to 2009.
"I can't imagine how he's feeling at the moment," Storm coach Craig Bellamy said of Papenhuyzen post-game.
"The amount of work he put in to get back to playing again, then get back into the NRL too.
"It wasn't a great night anyway, and it made it a lot worse."
Melbourne No.6 Cameron Munster was devastated for his teammate and good friend.
"I feel sorry for him. I probably saw the ankle out of the socket," Munster told the Nine Network.
"It is a bad injury run for him but hopefully he'll come back and we will see the Pappy that we know."Â
Xavier Coates will also have scans after he hurt his ankle in the second half, adding to the Storm's horror night.
"Our first half was really poor; we'd done well to be 8-0 at halftime, it could have been 20-0," Bellamy said.
"I'm not sure how we can come into this game and play like that.
"We just looked like 17 players thrown together on the night and 'good luck'.
"Our attack's been humming along OK, but tonight it looked like they just met each other in the dressing room before the game."
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