'Quad God' Malinin led the men's free skating final in Milan with Japan taking silver and host nation Italy claiming bronze after three days of competition.
Malinin hit five quadruple jumps but did not deliver the first ever quad axel jump in Olympic competition as he had promised.
The 21-year-old scored 200.03 to push Japan's Shun Sato into second place with 194.86.
Earlier Kaori Sakamoto's stunning women's free skate had put Japan ahead after Riku Miura and Ryuichi Kihara earlier hit a career-best pairs free skating performance.
The United States were the defending champions having been awarded the title at the 2022 Beijing Winter Games after Russian figure skater Kamila Valieva was handed a doping ban.
Russia had won the team title but were demoted to bronze when Valieva's points were deducted. Japan took silver in Beijing.