Joubert was in charge of the All Blacks' 20-6 victory over Australia in the semifinal last night.
It will be his first final and he becomes the second South African, after Andre Watson, to take charge of the final match of the global showcase.
"It is an enormous honour to get the final and I would like to thank (International Rugby Board referees manager) Paddy (O'Brien) and the committee for giving me the opportunity," Joubert said in a statement.
"I am now really looking forward to getting out there and enjoying the occasion."
England's Wayne Barnes will referee the playoff for third place between Australia and Wales on Friday.