A 35-15 win looks a straightforward-enough margin of victory but in many ways for much of the match it was Japan who had more to smile about.
"The first 50 minutes everything was going our way", said Japan captain Leitch, who had an outstanding game.
The score was levelled through Daly's penalty taken on the halfway line but Japan was soon back in front through a try from captain Michael Leitch that was a combination of magnificent running and terrible defense by Care, replacement Hartley, and Harry Williams.
George Ford, captain for his 50th cap, scored 12 points with the boot and Elliot Daly was on target with a long-range penalty in a first half which Japan dominated, but they were ultimately emphatically beaten.
"But we lost concentration for ten minutes in the second half and that cost us badly". We just needed to up it, they were beating us round the corner and winning the one on ones.
England, for their part, were grateful for the halftime turnaround.
In the first half Japan had 77 percent of territory and 69 percent of possession.
Tamura added the extras and although a monster Daly penalty from halfway levelled the game at 10-10, the Brave Blossoms responded with a brilliant individual try from skipper Leitch - breaking a tackle from a stationary position just outside the 22, bursting through and beautifully side-stepping last defender Daly for a 15-10 half-time lead.
Some good strength on the ball from Akihito Yamada freed up Leitch who beat four tacklers on his way to the line, before Nakamura made the most of Fumiaki Tanaka's bullet pass to go over from a scrum five meters out.
With the set piece starting to struggle and gaps appearing in their defense, Japan rarely threatened and England took a strangle grip on the game.
"When I brought them over to Europe we played Georgia, Romania and the French Barbarians", he said. "Scoring an early try, players sub-consciously think it's going to be easy and we knocked off a little but I thought our second half response was excellent". "They are a proper rugby country and I'm really pleased for them".
"The second half was fantastic - mentality-wise, attitude wise, we were a bit calmer in our positioning which allowed us to come back into the game". "The attitude was better and we played like England in the second half and the players will have learned a lot from that".
But as Joseph pointed out they still need to work on their discipline and accuracy.
"It's about changing the squad and looking at how we can improve", said Jones.