Ohtani prevailed in front of a sell-out crowd of 36,098 to spark wild celebrations both among his team-mates and back home in Tokyo.
"I think as a baseball fan, everybody wanted to see it. He won round one," said Trout with a smile.
"The baseball world won tonight," added US manager Mark DeRosa. "I was hoping it would go our way with Mikey popping one against Ohtani.
"The whole world got to see Ohtani come in - [in a] big spot, battling. That's kind of how it was scripted. I just wish it would have gone differently."
After striking out Mike Trout to clinch victory, Shohei Ohtani threw his glove and cap into the air before being mobbed by his team-mates
Philadelphia Phillies shortstop Trea Turner put the star-studded US team in front in the second inning with his fifth home run of the tournament, tying the record for a single WBC.
Munetaka Murakami homered to help Japan gain a 2-1 lead in their second inning, before Kazuma Okamoto homered in the fourth.
Kyle Schwarber hit a home run in the eighth inning to cut the deficit to 3-2, before Ohtani won his individual duel with Trout.
"Whether I got him out or he got a hit off me, I didn't want to take any risks," Ohtani said. "I wanted to make my best pitch.
"This really proves that Japanese baseball can beat any team in the world."
US manager DeRosa added: "Although our guys are disappointed, I couldn't be prouder of them, the way they came together as a team. They truly started to bond and enjoy being around each other."
The next WBC is due to be held in 2026 and Ohtani has challenged Japan to build on their success.
"Just because we won today doesn't mean that we achieved a final goal, this is just a passing point," he said. "Our team has just started."