Joubert, back this season after recovery from a major shoulder operation, injured a knee early in Otago's 20-17 loss to Northland in Whangarei on Saturday and left the field soon after.
Scans yesterday revealed damage that would sideline the South African flanker for the rest of the congested ITM Cup.
"It looks like it's a four to six-week injury, which will mean he's probably finished," Otago co-coach Phil Mooney said yesterday.
"It's so disappointing for Eben, because he's fought hard to come back from his shoulder.
"He's a real lead-from-the-front captain. So that means everyone else is going to have to step up in his absence."
Former All Black lock Tom Donnelly is the Otago vice-captain and the logical new skipper, with old hands like Kees Meeuws and Tony Brown providing support.
Mooney and Andy Hunter will have to decide between two rookie opensides in towering Kaikorai flanker Adam Hill and youngster TJ Ioane, who has been slightly erratic but has provided energy off the bench this season.
Another blow to Otago is the loss of second five-fullback Sam Giddens for "a while" with a hamstring injury.
That will be alleviated by the return of fullback Ben Smith, who it is understood has been released from his duties as All Black injury cover.
Utility back Glenn Dickson was scratched from the Northland game because he fell ill with a fever and vomiting the previous night, Mooney said.
It is a big week for Otago - and not only because it has to bounce back from consecutive losses.
The Razorbacks play Counties-Manukau at Carisbrook on Wednesday night, and then farewell the ground with a match against old rival and Ranfurly Shield holder Southland on Saturday.
"It's a pretty big responsibility," Mooney said.
"It's important we go out this week and give two performances that do the old ground justice."
