Los Blancos did not have things all their own way, however, being forced to battle back from a goal down to force extra time before eventually getting over the line thanks to Cristiano Ronaldo's brilliance.
Less than a week on from being crowned the world's best player, the Portuguese once again proved the difference for his side as Madrid added to their 2014 success in this competition and rounded off an impressive year under Zinedine Zidane in style.
European sides had won each of their last seven fixtures in this end-of-year competition without conceding prior to this match, and the omens looked good for the Spanish outfit when Karim Benzema - a member of that successful 2014 side - tapped home when Luka Modric's volley was parried into his path.
Madrid continued to dominate possession as the first half transpired, but Kashima - the first Asian side to ever reach the final - showed that it would not be all one-sided as Yasushi Endo fired in a shot that was blocked aside.
Modric was again denied by Hitoshi Sogahata 40 minutes in, who this time held on to the ball, but Antlers were soon up the other end and levelling things up after Gaku Shibasaki reacted quickest to a cross in the box and flashed a half-volley past Keylor Navas from eight yards out.
The La Liga pacesetters finally injected some urgency into their game after falling behind, earning themselves a leveller of their own after Lucas Vazquez was brought down inside the box and Ronaldo tucked the penalty into the bottom corner.
Sogahata tipped away another Ronaldo attempt on the hour, while Endo saw a shot easily kept out at the other end, but the best chance to win it in normal time fell to Benzema who could not convert from close range.
Kashima also had a couple of decent chances to win the contest, but their failure to beat Navas for a second time would prove costly as Ronaldo doubled his tally when picked out by Benzema, before slamming home a hat-trick three minutes later.
A buoyant home crowd urged their players on for one more late salvo, though it was not to be in the end as Zidane's men held out for another piece of silverware in Japan.