Nishimura, who had had a solid game up until that point, pointed to the spot after Brazil's Fred went down under the slightest of challenges from Croat defender Dejan Lovren.
Furious Croatian players surrounded the Japanese official, who responded by showing a stunned Lovren a yellow card.
After the dust had settled, Neymar, who had pulled Brazil level after Marcelo's 11th minute own goal, squeezed an unconvincing penalty past Stipe Pletikosa as the stadium erupted in celebration.
Image: Referee Yuichi Nishimura speaks to Dejan Lovren, Vedran Corluka and Sime Vrsaljko of Croatia after awarding a penalty kick
Photograph: Kevin Cox/Getty Images
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