There will be two phases of voting before the result is announced at around 17.30 GMT.
New Zealand hosted the World Cup in 1987, South Africa in 1995 while Japan hopes to host it for the first time.
The decision could be a sign of the commitment to expanding the game globally by rugby's authorities, with many in favour of Japan hosting the tournament.
South Africa's bid promises a spectacular showpiece and record profits of £69million, while large stadiums and being in the same time zone as the big European market are factors in their favour.
South Africa's ability to host a major event will be tested at the 2010 football World Cup but concerns have been raised about crime and security.
New Zealand is keen to win the rights for the World Cup after co-hosting the event in 1987 with Australia. They lost the right to do so again in 2003 after failing to provide assurances that venues would be clean of all advertising and sponsorship not connected to the World Cup.
The bid has drawn on the popularity of rugby union in the country and it successfully hosted the recent Lions tour.
However New Zealand's stadiums have limited capacity and the quantity of accommodation for visiting fans is a concern.
Japan, a minnow on the international stage, is hoping the need to spread rugby globally gives them hosting rights for 2011.
The country has hosted the 2002 football World Cup with four stadiums newly built for the competition.
The bid also has the backing of a number of big names including Martin Johnson, Jonny Wilkinson, and Nick Farr-Jones.
