South African Rugby Football Union chief executive Rian Oberholzer said the changes had been agreed with Australia and New Zealand.
“It will give the season a more logical progression with interest building throughout the year,” said Oberholzer.
The change will mean the Tri-Nations competition will take place in September and October (rather than July and August).
The Super 12 will be moved to July (rather than February) and domestic competitions such as South Africa’s Currie Cup and New Zealand’s National Provincial Championship will start in March and conclude in May rather than ending in October.
The current structure will remain in place in 2001.