Seferovic, battling for the role of Switzerland's lone striker at the World Cup, came on in the second half and finished off a well-worked move in the 82nd minute for his first Switzerland goal since September.
He exchanged passes with Xherdan Shaqiri, who then crossed to the far post for Francois Moubandje to head across goal where Seferovic turned the ball past Eiji Kawashima from close range.
The 26-year-old has had a miserable season for Benfica where he scored only four league goals and was left out of the squad altogether for a number of games.
He was also booed off by Switzerland fans after missing several chances in the second leg of their qualifying playoff tie against Northern Ireland in November which the Swiss won 1-0 on aggregate to qualify for Russia.
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Switzerland, who face Brazil, Costa Rica and Serbia in their World Cup group, went ahead with a bizarre penalty four minutes before halftime.
Breel Embolo burst into the penalty area, then clearly trod on the foot of a Japanese player but went tumbling over and the referee pointed to the spot.
Japan, who face Poland, Senegal and Colombia in their World Cup group, slumped to their third successive defeat after also losing to Ukraine and Ghana. They face Paraguay in a final warm-up on Tuesday.
(Writing by Brian Homewood in Bern; Editing by Toby Davis)
