The key purpose of the week-long visit is to undergo research and testing of the Rugby World Cup 2015 apparel at the ASICS Institute of Sport Science in Kobe.
SARU CEO Jurie Roux and Springbok coach Heyneke Meyer are leading a delegation of 12, including eight Springboks in Jean de Villiers, Bismarck du Plessis, Pat Lambie, Tendai Mtawarira, Willie le Roux, Duane Vermeulen, Eben Etzebeth and Cornal Hendricks, as well as members of management.
As part of their visit to Japan, the Springboks will also conduct a coaching clinic at a school in Nara, and visit the ASICS Corporation Head Office and ASICS Sports Museum.
Typhoon Vongfong, the strongest storm to hit Japan this year, has made landfall on the country's main islands, forcing more than 300 flights to be cancelled and hundreds of thousands of people to evacuate their homes.
Vongfong, which means wasp in Cantonese, currently has winds of up to 120km/h, with gusts of 175km/h.
Springbok flyhalf Pat Lambie tweeted a picture on Monday of Eben Etzebeth, Cornal Hendricks and Bismarck du Plessis feeling the full force of the typhoon.