Nacional's players reacted furiously after Hungarian referee Viktor Kassai referred to the new technology in Osaka following complaints from the Kashima bench protesting that Daigo Nishi had been tripped on the half hour mark.
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Shoma Doi made history by converting the penalty before Yasushi Endo added a cheeky back-heeled goal and substitute Yuma Suzuki completed the rout late on, Suzuki striking a Cristiano Ronaldo-style pose in celebration.
The Antlers, who become the first Japanese team to reach the final, face either Ronaldo's Real Madrid or, in the event of a seismic shock, Mexico's Club America for the title of the world's best club team on Sunday. Those two sides meet in Yokohama on Thursday.
Video technology is being trialed in FIFA competitions for the first time at the Club World Cup in Japan.
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The system involves assistant referees monitoring television screens and relaying information on so-called "match-changing decisions" to the match officials during the game.
"They kept attacking relentlessly," Antlers coach Masatada Ishii told reporters. "I'm just relieved we held out. We hung in there and we've got our reward, we're in the final now. We will be fighting for all of Japan."
On the other hand, losing team’s manager bemoans the controversial goal, after which, according to him, the team lost its organization. "We lost our organisation after that first goal," said Nacional coach Reinaldo Rueda.
"Maybe we were too confident. It's a harsh lesson but one we must learn from to improve."
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