Medina, who had scored a rare 10 in his quarter-final, made the most of perfect conditions at Pipeline to secure 9.10 on his best ride to give him a two-wave total of 16.27.
Needing a 7.78 to get in front of the Brazilian, Smith waited anxiously for one more wave to arrive but never got his chance as time ran out leaving him on 15.83.
"This means a lot to me," Medina said in a beachside interview after being mobbed by fans as he emerged from the surf.
"I put in a lot of work this year. It was an intense year, everything paid off. I can't find words at the moment.
"I'm so happy to win it again, go Brazil!"
Medina continued his fine form in the final with a best ride of 9.57 on his way to a 18.34-16.70 victory over Australian Julian Wilson to wrap up the season with a third victory - the first of his career at the prestigious Hawaiian break.
"This is out of order," Medina grinned after again being mobbed by fans and chaired off the beach at the spiritual home of the sport.
"All my big heroes have won this title. The Pipe Master's a little different, I really wanted that one."
Wilson, who beat 11-time world champion Kelly Slater in the semi-finals, also finished second in the championship ahead of Medina's compatriots Filipe Toledo and Italo Ferreira.
"Everyone is pushing the limits, the level was really high this year," Medina added after clinching the title.
"All the boys are pushing me to train more, to surf more. That's my motivation. It's been a long year, really intense."
(Reporting by Steve Keating in Toronto. Editing by Nick Mulvenney)
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