The Swedish team announced it would part with Nykjaer - who has scored three wins this year and lies third in the drivers' championship - in the build up to this weekend's Suzuka round.
The 33-year-old Japanese driver has already made occasional appearances in the WTCC, having driven a SUNRED SEAT in each of the past two seasons at Suzuka.
GP2 podium finisher Yoshimoto, who leads the ST3 class of this year's Super Taikyu series, will miss the Shanghai WTCC round before returning for the Macau finale.
"We are obviously disappointed not to be able to complete the season with Michel, but we've already achieved great things together this season, which was meant to be a pure learning year," Nika team manager Nicklas Karlsson said.
Series regular Franz Engstler has meanwhile been forced to withdraw from Suzuka due to illness.
His eponymous team has drafted in Masaki Kano for the Japanese round, with Engstler expected to return at Shanghai in November.
Kano, 37, has never missed a WTCC event in Japan, and has contested his home race with the Engstler squad since 2008.
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