He officiated at his first Super 12 match in Sydney when the New South Wales Waratahs beat the Chiefs 25–7 in the opening round of the competition.

[19] He once again took charge of a match between Australia and New Zealand in the 2010 Tri Nations Series[20] and was appointed to officiate the final of the 2010 Currie Cup Premier Division between the Sharks and Western Province in Durban.

[23] He was named on the refereeing panel for the 2011 Rugby World Cup,[24] and took charge of four matches during the pool stage of the competition.

[29] Gerry Thornley, writing in The Irish Times, was of the opinion that France was the better team on the night, with Joubert being reluctant to award penalties against New Zealand in the last quarter of the match.

[30] Sir Clive Woodward was of the same opinion [31] In 2012, Joubert took charge of the 2012 Six Nations Championship match – and Grand Slam decider – between Wales and France[32] and was also involved in the very start of the 2015 Rugby World Cup qualifying tournament, as he officiated the first match between Mexico and Jamaica in the Americas qualification tournament.

[45] He refereed several matches in the 2014 Currie Cup Premier Division, including the final between Western Province and the Golden Lions.

[47] He was named on the refereeing panel of the 2015 Rugby World Cup[48] and took charge of four matches during the pool stage of the tournament.

This was criticised by Scotland supporters, as well as former players like Andy Nicol and Matt Dawson,[50] after replays showed that Joubert had awarded the penalty erroneously.

[54] Joubert ended the game and immediately ran to the tunnel without shaking hands with any players or his team of officials.

[55] However, this public review of Joubert's performance also attracted criticism from figures within the game, such as Australia coach Michael Cheika and former player David Campese.

[56][57] In addition, Joubert was also criticised by former Scottish captain Gavin Hastings and former Scotland winger Kenny Logan for rushing from the field immediately after the match ended, rather than shaking hands with the players and fellow officials, as is tradition.