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.
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 Japanese team to reach the final, face either Ronaldo's Real Madrid or Mexico's Club America for the title of the world's best team on Sunday.
Video technology is being trialed in FIFA competitions for the first time at the Club World Cup in Japan.
The system involves assistant referees monitoring television screens and relaying information on so-called "match-changing decisions" to the match officials during the game.