Joubert, normally an openside flanker, will start on the blindside flank for Otago, replacing Adam Thomson, who is on All Black duty.
Hoani Matenga moves into lock to replace Tom Donnelly, who is also away with the All Blacks though not required for the test against South Africa.
Glenn Dickson wins the first five-eighth position ahead of Michael Witt, with confirmation Chris Noakes, who wore the No 10 jersey for Otago in the first five games of the season, is out for a month with an injured groin.
No 8 Steven Setephano changes places with Paul Grant.
Winger Fetu'u Vainikolo moves on to the reserves bench after recovering from a knee injury, but fails to dislodge Ryan Shortland and Karne Hesketh from starting.
Otago coach Steve Martin said Joubert had been selected for his work at the breakdown, which was a vital part of the game.
"Eben has that ability to be competitive in the loose and possesses some of those qualities at the breakdown which are very valuable," Martin said.
"Adam has really shone there this year for us and hopefully Eben can keep that up."
Joubert has not even made it to the Otago reserve bench so far this season, and his lack of height may be a factor at lineout time against a Canterbury side which has former lock Michael Paterson on the blindside flank.
Martin said Setephano could jump at the back as could captain Alando Soakai, and Grant could come on from the bench.
Joubert has been in good form for Otago B and Martin said Matenga, who has played a lot of rugby at loose forward, had experience at lock, and should have no problems with the position.
Martin said it was a close call to pick between Dickson and Witt, but Dickson had impressed in his first start against Auckland last week.
"But Michael has that ability to come on and change the complexion - the way the game is played. He showed some really nice touches last week."
Witt is likely to see some game time.
Prop Ben Nolan was available for selection after getting over a rib injury, but Otago has gone for Sam Hibbard and veteran Kees Meeuws in the front row, with Keith Cameron on the bench.
Martin said the side was excited about having a second challenge, and had trained well this week.
He was expecting a Canterbury side eager to bounce back from a disappointing defeat against Bay of Plenty, and defending the Ranfurly Shield at home for the first time in this tenure.
Canterbury has called big centre Casey Laulala on to the bench, as he works his way back to full fitness after breaking an arm earlier in the season.
Apart from Laulala, coach Rob Penney has named two other All Blacks on the bench, halfback Andy Ellis and hooker Corey Flynn.
Captain George Whitelock has recovered from an ankle sprain and will take the field, alongside his brother Sam, who locks the scrum with the returning James Broadhurst.
