But they will savour the defeat of New Zealand, just as they did when they toppled the Springboks at the Rugby World Cup.
"It was unbelievable," said Japan back Lomano Lemeki. "You never think you would see a minnow team come here and beat a gold medal contender.
"I'm still shocked to be honest."
Williams was ruled out for the rest of the tournament with the serious injury after he took a crash ball into two defenders early in the second half.
The woes did not end there with Joe Webber dislocating a shoulder in the defeat. Captain Scott Curry said they were guilty of making too many mistakes.
"Without the ball it's pretty hard to score and when we got it we knocked it on or turned it over at the ruck."
Playing well above themselves, the underdogs scored the opening try but the Kiwi side led 12-7 with two minutes to go before Kameli Soejima crossed out wide and Ktsuyuki Sakai nailed a clutch conversion.
NZ almost stole the match at the death with a 90m raid after the siren but heroic defence ultimately ensured another fairytale result.
"That was crazy," Lemeki said. "Everyone was flying just like a kamikaze plane trying to chop their legs off - as long as we didn't let them score a try, if we got knocked out that's fine."
It was one of three upsets on captivating day one of the men's sevens with Australia falling 31-14 to France and Argentina also surprising USA 17-14.
"It means any team can win on any day in sevens," Lemeki said. "It's wide open."