Plushenko, a three-time medalist and the Olympic champion eight years ago, was forced out of the competition by back pains.
The 31-year-old Plushenko had complained of problems in his back after his long program routine in Russia's march to the inaugural Olympic team figure skating championship last weekend.
He chose not to go through his last formal practice session due to concerns over his back and when he took to the ice for his warmup prior to Thursday's competition he quickly discovered he could not compete.
After landing a jump in the warmup period, Plushenko reached for his back and immediately skated to the area where the nine judges and the referee were sitting. He told them he was through for the Olympics and, since he has said this would be his farewell to the sport, it is assumed he is through with his career as well.
Plushenko has won three world championships and has been European champion seven times. Although the last of his world titles came a decade ago, he has remained a force in the sport. His performance in the team event earlier in the Olympics showed he was a threat to win gold at these Games.
Hanyu, fourth at the most recent world championships, was given 101.45 points for his routine. Patrick Chan of Canada was second at 97.52 and Javier Fernandez of Spain was third at 86.98.
American Jason Brown finished sixth and teammate Jeremy Abbott was 15th after falling hard and slamming into the wall head first. Abbott, who also fell during the team event, stumbled coming out of a jump and the toe of one of his skates dug into the ice sending him sprawling.