Nery (24-0) scored a fourth round technical knockout in the Aug. 15 bout in Tokyo but has since been under investigation after an out-of-competition sample tested positive for the banned substance Zilpaterol.
Nery and his camp denied the boxer had taken any performance-enhancing drugs and did not request a B sample analysis, the WBC said.
"...the WBC cannot make a determination with sufficient certainty as to whether Mr Nery's adverse finding was the result of intentional ingestion of a banned substance to improve performance," the governing body said in a statement.
"The WBC hereby orders an immediate rematch between Mr Nery and Sinshuke Yamanaka..." it added, without changing the result of the original bout.
Yamanaka's promoters had earlier said the 35-year-old would quit boxing if denied a chance to fight Nery again after losing his first professional fight to the Mexican in his 13th title defense.
"I've been thinking that I don't want to end my career," Yamanaka (27-1-2) told Kyodo news. "I want to get back at him."
(Reporting by Amlan Chakraborty in New Delhi; Editing by John O'Brien)
