With the European champion trailing 2-1 in the second half, Ronaldo leveled with a 60th minute penalty and scored the two further goals in extra time to seal its victory.
The Antlers, the first Japanese side to reach the final of the inter continental competition, gave Real an almighty scare in front of partisan home support, despite going into the title match as a heavy underdog.
When Karim Benzema put the Spanish side ahead as early as the ninth minute, it looked ominous for the Antlers, who had stunned South American champion Atletico Nacional of Colombia 3-0 in the semifinal.
But just before halftime, Gaku Shibasaki's fine left foot volley leveled the scores and changed the complexion of the game.
The second half was just seven minutes old when Real caption Sergio Ramos made a hash of a clearance and Shibasaki returned it with vengeance to power his shot past Keylor Navas and to give the Antlers the lead.
Until to that point Ronaldo had been largely subdued, but when Lucas Vazquez won a penalty after being fouled by Shuto Yamamoto, he stepped up to level from the spot.
That was not the end of the drama, with Navas having to make crucial saves to deny Kashima a late victory and Ramos lucky not to be sent off while on a yellow card.
Early in extra time, Benzema released Ronaldo to score his second before Shibasaki's free kick was headed against the Real crossbar by Yuma Suzuki from close range.
The miss proved vital and within minutes Ronaldo had seized on a scuffed shot from Toni Kroos to complete his hat-trick and round off Real's second victory in the Club World Cup.
"What a game," said Ronaldo after helping Real extend is unbeaten run to 37 games, 26 from the start of this season.
"We had to suffer, but that's what finals are about," he added.
Atletico takes third spot
Earlier, Atletico Nacional beat Club America 4-3 on penalties to finish third, completing a tumultuous three weeks for the reigning Copa Libertadores champion.
Miguel Borja scored the decisive penalty after his side had seen a two-goal lead evaporate against its Mexican rival.
Atletico had been due to play Chapecoense in the final of the Copa Sudamericana last month, but a plane crash saw all but a few of the Brazilian team killed on the way to the match.
Fans in Yokohoma cheered the Atletico team in the playoff, many waving Chapecoense flags in tribute to the fallen side.
Barca chase Real
In European league action later Sunday, Real Madrid's arch-rival Barcelona won its city derby against Espanyol 4-1.
A Luis Suarez double put Barca well on the way to victory before Lionel Messi set up Jordi Alba for the third.
Espanyol pulled a goal back before Messi completed a comfortable win which takes the Catalans to within three points of Real at the top of La Liga.
In Germany, a long-range Douglas Costa effort gave Bayern Munich a 1-0 win at Darmstadt to take over again at the top of Bundesliga from RB Leipzig on goal difference.
The two leaders play a crunch game Wednesday in the Allianz Arena.
In the EPL, Manchester City hit back from an early Theo Walcott goal to beat Arsenal 2-1 with Leroy Sane and Raheem Sterling scoring. The win lifted City to second, but seven points behind leader Chelsea.
Ligue 1 leader Nice stayed at the summit in France as Mario Balotelli scored twice in a 2-1 win over Dijon.