Joubert will also take charge of Ireland's clash with Russia in Rotorua on September 25. The game against Australia in Eden Park will be refereed by New Zealander Bryce Lawrence, who like Joubert is making his Rugby World Cup refereeing debut.
South African Jonathan Kaplan will have the whistle for Ireland's final pool fixture against Italy in Dunedin on October 2.
Irish referee George Clancy has been awarded the opening match of the tournament between hosts New Zealand and their Pacific Island neighbours Tonga.
Clancy will also be in charge of the games between Scotland and Georgia and Ireland's pool rivals Italy and the USA, as well as the clash between South Africa and Namibia.
Alain Rolland, who refereed the 2007 Rugby World Cup final, will also be in charge of a game in Ireland's pool when Australia face Italy.
Rolland will referee three other ties in the pool stages - Wales v Samoa, Argentina v Georgia and the possible pool decider between New Zealand and France.
The appointments were made by the IRB's Match Official Selection Committee, which is chaired by IRB Council Member David Pickering.
Each of the 10 referees selected for rugby's showcase tournament will take charge of four matches during the pool phase.
Pickering said: "In selecting a streamlined referees panel, we are committed to an approach that promotes consistency and ensures that the best referees are selected for the world's best teams playing in rugby's premier tournament.
"Each referee will take charge of four matches during the pool phase allowing for a comprehensive review of performances by the Selection Committee. A total of 10 of the 21 match officials will be retained for the knock-out stages."
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