Hanyu earned a total score of 317.85, his hold on first not in much doubt with two skaters to follow after a relatively clean if not transcendent program. Countryman Shoma Uno scored 306.90 to take silver, while Spain's Javier Fernandez secured bronze with 305.24 points.
American Dick Button went back-to-back in the men's discipline in 1952.
Toronto's Patrick Chan was sitting sixth heading into the free skate, but he fell to ninth overall at 263.43.
Keegan Messing of Sherwood Park, Alta., dropped from 10th to 12th with a total of 255.43.
Chan, competing in his third and final Games, was happy with a performance that he acknowledged as solid, but not perfect.
"My goals coming into these Games, I've accomplished and today my small little goal was to land both Axels and I did that," Chan told CBC Sports' Paul Martini.
"A lot of guys really laid it down today, so all I could do was focus on my own challenges. I didn't need the additional weight of trying to think about beating these guys. I just took it one thing at a time and I had a great skate. I can step off the ice feeling really happy about myself."
Chan, 27, said his proudest accomplishments include helping Canada to gold in the team event in Pyeongchang as well as his 10 national titles. He also took home silver in both the men's competition and team event at the Sochi Olympics.
Chan also opened up about some challenges he faced in recent years that had him questioning the idea of going to the Olympics at all.
"This past year and the year before were really challenging – going as far as not even wanting to make it to these Games and moving on and going on to other great things," he said after the free skate.
"But I am so thankful for the people I had around me … they've all been there every step of the way, believed in me more than I believed in myself. I learned a lesson and now I step off the ice here feeling like I believe in myself and have confidence in myself."
Chen jumps into record books
Meanwhile, Nathan Chen of the U.S. turned in a record-setting performance by landing six quadruple jumps to redeem a pressure-filled performance in the short program.
The 18-year-old vaulted from 17th to fifth as he nailed virtually every element in the free skate along the way to a total score of 297.35.
Even though he touched down on his sixth quad attempt, Chen's technical score of 127.64 helped vault him into contention. His 215.08 points for the free skate, in which he did not receive any deductions, eclipsed his previous personal best of 204.34.
Chen's personal-best overall score is 307.46 which he established at the Four Continents Championships in February 2017.
The two-time U.S. champion — widely regarded as his nation's best hope for a figure skating medal in Pyeongchang — had succumbed to the pressure and massive expectations in Friday's short program. He fell on all of his jumps and scored 82.27 (well below his best mark of 104.12) to plummet to 17th out of 24 skaters heading into the free skate.
"As much as I tried to deny it, I think I did feel the pressure a lot, thinking about medals and placement and things like that, things that were entirely out of my control," said Chen. "That just tightened me up, made me really cautious on the ice, and that's not the way to skate."