Japan's Yuma Kagiyama took silver and countryman Shun Sato captured bronze on a night when many top skaters struggled to execute their jumps.
"I blew it," Malinin told NBC after finishing a shocking eighth.
"That's honestly the first thing that came to my mind. There's no way that just happened. I was preparing the whole season and was so confident in my programme, so confident with everything. I have no words really."