Joubert (29) has two prolapsed discs at the base of his neck and has been warned another heavy blow to the area could have dire consequences.
The respected and talented loose forward will be a tremendous loss to Otago, especially as new coach Tony Brown is trying to develop an inexperienced team from the ashes of the union's brush with liquidation.
Joubert said he had taken a "few shots" to his neck during the club season. A couple of weeks ago, he woke up the day after a game feeling particularly tight.
"I got some scans that said the discs between the vertebrae were pushing against nerves," he said.
"They're actually touching my spinal column, so I got told a big shot could spell paralysis.
"You hear something like that and it kind of whacks you in the face. It makes you think about your mortality.
"Or not so much your mortality, but the reality that your sporting career can be all over, at any stage."
At this stage, Joubert is out for 12 weeks. The neck had to settle because it was in the dangerous acute phase, he said.
The injury would be monitored and another scan would take place in a month, to see if surgery was necessary.
"So it's a season-ending injury, and potentially a career-ending injury.
"That's something I will have to consider after more consultation with the doctors."
Joubert's recent career has been blighted by injury - he has just 18 first-class appearances for Otago over four seasons - but he pointed out his early years were free of major problems.
His first major injury was the shoulder he dislocated in the Ranfurly Shield challenge in Invercargill two years ago. Last year, he blew out a knee.
"I play a high-risk game, in a high-risk position. That's how I grew up and that's how I learned the game.
"Years ago, I made peace with the fact I could only play one way, and that my career would probably end before I wanted it to, because my body told me to stop.
"I've got so many good memories of rugby, and I don't want to spoil it. So if it's time to walk away, then I have to deal with that.
"I won't feel sorry for myself. I'm bloody lucky. I'm 29, I've had 10 good years of rugby, and I've achieved a lot.
"I would have loved to play for the Highlanders, and win the Ranfurly Shield with Otago. But I've been given some amazing opportunities, and for that, I will always be grateful."
Joubert dreamed of playing Super rugby but knew he had not done enough to convince Highlanders coach Jamie Joseph.
"I know I was good enough," he said.
"But I can't for one second hold it against Jamie. I just hadn't played enough rugby. I wouldn't have picked me if I was in his shoes."
Joubert is originally from South Africa, where he played senior rugby for the University of Pretoria, and for the Blue Bulls in the Vodacom Cup.
He came to Dunedin in 2008, joining the Harbour club.
South Africa is still home but Joubert has fallen in love with Otago, and wears the blue jersey with as much pride as anyone.
It hurt him to watch the union's financial near-collapse, but he remains excited about Brown's plans and hopes to remain with the team in some sort of off-field capacity.
"It's a huge rebuilding phase for Otago. It's going to be tough but it's also really exciting to have local young players coming through, and the right people like Browny in place."
Brown will need to find a new captain. Paul Grant or Glenn Dickson are the likely contenders.
For Joubert, the thought of life after rugby now becomes more prominent.
He spent three months in England working for the BBC as part of his MBA earlier this year, and is doing some consultancy work.
His German girlfriend, Melanie, will soon join him in Dunedin.
