Nacional's players reacted furiously to a penalty that was awarded against them by Hungarian referee Viktor Kassai.
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, in the event of a seismic shock, Mexico's Club America for the title of the world's best 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.
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."
Kashima were fortunate not to be at least three goals down before the penalty incident, Nacional forward Jhon Mosquera going closest for the Colombians with a ferocious volley which rattled the crossbar.
Antlers goalkeeper Hitoshi Sogahata was forced to make several sharp saves before Mosquera smashed another shot against the bar just before halftime as the Libertadores Cup holders went in search of the equaliser.
The Colombian players continued to remonstrate as they trudged off, complaining -- with some justification on the evidence of television replays -- that Orlando Berrio had clipped Nishi's heel by accident.
Nacional had been the tournament's sentimental favourites due to their incidental connection to the recent air tragedy that decimated Brazilian rivals Chapecoense, whose flags and replica shirts were waved in tribute by Atletico fans in Osaka.
Chapecoense had been on their way to play the Colombians in the final of the Copa Sudamericana when their plane crashed into a hillside near Medellin last month, claiming 71 lives, including all but three of the Chape players.
Earlier Wednesday, South Korea's Jeonbuk Motors thrashed South African side Mamelodi Sundowns 4-1 to win the fifth-placed playoff.