Prop Nyakane was sent on for Frans Malherbe in the second half of the 41-7 victory in Kumagaya but was forced off just 14 minutes later.
However, the 30-year-old did not sustain a serious injury and is expected to be available when the Springboks begin their World Cup campaign against reigning champions New Zealand on September 21.
"The tighthead prop sprained a knee during the 41-7 victory over Japan in Kumagaya on Friday and was limited to a 14-minute appearance," read a statement from the Springboks.
