The process will be reversed for the third leg before the race continues to Sanya in China.
It is the first time the round-the- world race has had to be effectively cut short because of the threat of pirates.
Race director Jack Lloyd said it was unfortunate that organisers had to take those measures but, after taking advice from government and marine agencies, they came up with the best possible alternative to ensure the sailors' safety.
Piracy was a well-organised and lucrative business and had expanded into a vast area off the coast of Somalia. Last year a record 1181 seafarers were kidnapped for ransom by pirates.
"It is still very much a race around the world and we believe we have found a fair points system that will help make it an exciting sprint into Abu Dhabi," said Lloyd.
"The teams all understand the situation and have given us their full support."
The scoring system has been modified so that 80 per cent of the points of Leg 2 are based on the race between Cape Town and safe haven 1 and 20 per cent for the sprint into Abu Dhabi.
Team New Zealand were second out of Table Bay on Sunday morning after the inshore aspect of the leg in a steady localised 15 to 20 knot southwesterly breeze. But that breeze softened yesterday, leaving the fleet facing unstable weather over the next few days.
The tactical minefield as the boats head southeast around the Cape of Good Hope and into the Indian Ocean offers a real headache for navigators but also the opportunity, if picked correctly, to cement an advantage over the rest of the fleet.
Skipper Chris Nicholson said the team were ready to make the most of the conditions.
"We rate our ability to do well in light and fickle conditions and are absolutely focused on turning them to our advantage."