Hagino clocked 4min 06.05sec, holding off American Chase Kalisz to wrest the title from US hands, where it had rested for the past five Games.
Kalisz clocked 4:06.75 and Japan’s Daiya Seto was third in 4:09.71.
Hagino’s time made him the third-fastest performer in history behind world record-holder Michael Phelps and 2012 Olympic champion Ryan Lochte.
Neither of those US stars were in action on Saturday, Phelps opting out of the gruelling event he dubbed “swimming’s decathlon” and Lochte failing to qualify at the US trials.
Kalisz had led the way into the final in a spirited preliminary duel with Seto, while Hagino, swimming in a different heat, cruised to a victory with plenty in the tank for the final.
He seized the lead on the second, backstroke leg and never relinquished it, as Kalisz battled past Seto on the breaststroke leg and pushed Hagino to the last wall on the closing freestyle.