Joubert took charge of his first Test when Namibia faced Uganda in 2013 and went on to hold the whistle in 69 international matches.
The South African, who will continue to officiate on the rugby sevens circuit, where his experience includes refereeing at the Olympic Games in Rio last August, will take up the position of referee talent development coach at the sport’s international governing body from next year.
Joubert said in a statement: “This was not a decision I took lightly given the obvious lure of possibly refereeing the British and Irish Lions in New Zealand next year as well as the Rugby World Cup in Japan in 2019.
“However, the opportunity to make a difference in other peoples’ careers and lives is something which I’m excited about. It really is a dream job.
“Over the past few years I have taken [South African referee] Rasta Rasivhenge under my wing and have mentored and coached him and it has been enormously rewarding to see him grow as a person and as a referee.
“This position gives me the opportunity to play a more formal role in sharing my experiences and developing referees and to have a positive influence on the lives and careers of other young referees.
“I am also thrilled that I will continue to referee on the World Rugby Sevens Series as we build our team of referees towards the Tokyo Olympics in 2020. I love the sevens environment and being a part of this very special team.”