Shoma Doi converted a historic penalty on 33 minutes, the first spot-kick to be awarded with Video Assistant Referees (VARs) assisting the referee in a FIFA competition, before Yasushi Endo and Yuma Suzuki bagged two late second-half goals to send the J1 League champions into the global club showpiece final.
Kashima have made history by becoming the first Japanese team to reach the Club World Cup final and will face the winner of Club America-Real Madrid, who meet in the second semi-final to be contested on Thursday in Yokohama.
In an action-packed first half which saw Atletico Nacional dominate possession and chances, Miguel Borja saw a threatening right-footed volley saved on 21 minutes, before Mateus Uribe's effort moments later flew inches shy of the post. Jhon Mosquera then hit the crossbar for the 2016 Copa Libertadores winners, while Orlando Berrio's scissor-kick was cleared of the line by Gen Shoji on 23 minutes.
Despite Colombian dominance, it was Japan's top dogs Kashima who took the lead on 33 minutes. A historic spot-kick was awarded when VARs were used to assist referee Viktor Kassai with a match-changing decision for the first time in a FIFA competition. Kashima were awarded a penalty when Daigo Nishi was adjudged to have been brought down inside the area and Doi made no mistake from the spot, firing Kashima in front.
The side from the Tohoku region went close moments later when Naomichi Ueda was denied by a diving left-handed save from goalkeeper Franco Armani.
Atletico Nacional relentlessly pressed for an equaliser as the first half progressed. Berrio turned two defenders to break into the box and shoot, but Hitoshi Sogahata produced a marvellous stop to keep his side in the lead. Then, shortly before the break, Jhon Mosquera rattled the crossbar with a thunderous effort.
In the second half, the Colombians continued to look dangerous going forward. Borja charged into the box and tried to squeeze an effort past Sogahata at the near post, but the shot-stopper was quick to parry the ball away. Substitute Cristian Dajome then blasted an effort over the bar after a wayward shot landed in his path in front of goal.
After Alejandro Guerra charged into the area and had a close-range effort denied, Kashima grabbed a second through Endo, who took a lovely touch past goalkeeper Armani after receiving the ball in the centre of the area, turning and back-heeling the ball into the net.
Before Atletico Nacional had a chance to respond, they found themselves trailing by three goals. Substitute Mu Kanazaki, proving a handful with his threatening runs in the second half, launched a low ball across the face of goal, where Suzuki was waiting to tap home at the far post.
Alibaba YunOS Auto Player of the Match: Hitoshi Sogahata (Kashima Antlers)