Kashima also became the very first team to benefit from a video replay in a Fifa competition.
Hungarian referee Viktor Kassai halted the game after his assistant alerted him to an incident inside the box in the 31st minute.
After viewing footage on a pitchside monitor he awarded a penalty to Kashima.
Up stepped Shoma Doi, who slotted home the spot-kick to give his J1 League side the lead.
Although Atletico dominated much of the game Kashima would scored two late goals to seal a comprehensive victory.
The second came from Yasushi Endo with seven minutes left.
Endo took full advantage after winning a duel with the goalkeeper to cooly backheel into an open net and double the lead.
Two minutes later Yuma Suzuki added a third for the Antlers tapping home a low cross to seal the win and a final showdown on Sunday with either the Spaniards of Real Madrid or the Mexicans of Club America. (Euronews)