New Zealand head coach Ian Foster has also seen hooker Dane Coles return home after he went down with a calf injury in the warm-up in Tokyo.
It means the All Blacks will need to appoint a new leader for their clash with Wales at Principality Stadium on 5 November. To further complicate the picture, lock Brodie Retallick was sent off for a dangerous clear-out at a ruck.
He was set to win his 100th Test cap in the Welsh capital but will now be subject to a disciplinary hearing. Foster has called-up Billy Harmon to replace Cane and Asafo Aumua to take over from Coles.
Better news for Foster is that wing Leicester Fainga’anuku will be rejoining the tour party after leaving camp in Japan for family reasons.
“It’s the reality of rugby, you always want to get through your first couple of games injury free. It hasn’t worked out this way, and it doesn’t change the challenges coming up,” said Foster
The 30-year-old Cane was involved in a head clash with teammate David Havili as the pair attempted to clean out a breakdown with 10 minutes to go. He said he knew immediately things weren’t quite right, yet still remained on the pitch for the rest of the match.
“I got up a bit slow and I knew, without having done my cheekbone before, that I had probably done my cheekbone. I could feel it when I put my hand to my head, and I could feel the blood in my mouth,” said Cane.
“Because it wasn’t too sore and there was only 10 minutes to go, I wasn’t too concerned. But I knew in that moment that it wasn’t too good.
“The game was in the balance at that point. It didn’t restrict my ability to play and perform, so I was happy to carry on.”
A visit to a local hospital for a CT scan later revealed two fractures, one below his left eye, and another off to the left of it. His tour was over, and he will have to see a specialist upon his return to New Zealand to determine whether surgery will be required to repair the breaks.
“I was really looking forward to these next few games and looking forward to hopefully finishing the year really strong as a team, as a captain and as an individual,” he added.
Japan caused the All Blacks plenty of problems at the line-out and were well in the game from start to finish. A scrappy first-half was characterised by neither side being able to keep possession for long periods.
Takuya Yamasawa kicked Japan into the lead before Retallick dived in for the first try. That sparked the All Blacks, who moved into a 21-3 lead with further tries from Braydon Ennor and Sevu Reece.
But Japan conjured up two tries of their own to make it 21-17 at the break. Caleb Clarke scored at the start of the second half for the visitors, but then Warner Dearns grabbed a charge-down effort for the Brave Blossoms.
Hoskins Sotutu added a fifth try for the All Blacks from close range before Retallick received his marching orders for a dangerous clear out at a ruck 13 minutes from the end.
Japan put New Zealand under the cosh for much of the rest of the game and got over for another try from Kazuki Himeno with a minute left on the clock to make it 35-31.
Richie Mo’unga, who had converted all five tries, then kicked a penalty after the hooter to ensure that Foster’s men held on to win.