The 2.08-metre tall Stormers forward, who has 29 Test caps for the Springboks, will join former national team-mate Jacques Fourie at Kobelco Steelers and will not be available for this year's Rugby Championship tournament at the least.
"It was a tough decision for me to make," Bekker, 29, said. "I've spent my entire professional rugby career in Cape Town but, at this stage of my life, I felt it would be best to further my career abroad and to embark on a new adventure."
The mobile second rower made his Stormers debut in 2005 and is three appearances away from becoming the first player to reach 100 for the franchise.
Cash-rich clubs in Japan have been able to lure away some of rugby's top talents in recent years.
All Blacks Sonny Bill Williams and Ma'a Nonu, Springbok Fourie du Preez, former Australian greats George Gregan and Stephen Larkham, and Welsh winger Shane Williams have all played in the country that will host the Rugby World Cup in 2019.