Plushenko justified his controversial inclusion in the Russian team with a rousing performance to Tango de Roxanne which he opened with a high-flying quadruple toeloop-triple toeloop combination.
But at 19, Hanyu eclipsed his 31-year-old rival with a flawless programme in which his jumps were higher, spins were quicker and footwork was immaculate.
His score of 97.98 was 6.59 points higher than second-placed Plushenko while Canada's Patrick Chan failed to live up to his favourite's tag after a botched triple Axel left him trailing in third.
The U.S., who are also considered medal contenders, are lagging behind in seventh after Jeremy Abbott had a day to forget by messing up every one of his jumps.
The team event features 10 nations and each country has one representative competing in men's singles, women's singles, pairs and ice dancing. They each perform a short programme after which the top five nations progress to perform a free skate.