Joubert started his career at the Boland Cavaliers where he played from 1999 to 2001 when he joined Western Province from 2002 to 2006. He made his debut for South Africa against New Zealand in 2001 and in that very game, picked up a serious knee injury. Despite several injury setbacks (one of which, a badly damaged shoulder, kept him out of the 2003 World Cup), Joubert continued to develop into a world-class centre.
He was a member of the 2004 Springbok squad that won the Tri-Nations. In the Boks' home match at Ellis Park in Johannesburg against the All Blacks, he became only the second Springbok in history (after Ray Mordt in 1981) to score a hat-trick of tries against the All Blacks. Joubert was also for a time South Africa's leading try scorer in Tri Nations play, with six tries, before being overtaken by Breyton Paulse.
During the 2006 Super 14 season. Joubert's form dipped dramatically due to several injury problems. Firstly he struggled with a back injury that kept him from playing in the Currie Cup. He then sustained a back injury that kept him out of the Currie Cup and the Springboks' year-end tour to Argentina, Wales and France. He returned to play for the Stormers in the Super 14, only to break his hand in their final fixture. On 11 September 2006, the Cheetahs announced that Joubert had signed for them for the upcoming 2007 season, thus ending Joubert's 5-year association with the Stormers and Western Province Rugby Union.