Dylan Hartley's late try then ensured the scoreboard flattered England, but it could not mask a performance that lacked the intensity, ambition and executive of their previous performances against South Africa and New Zealand.
Admittedly, England had made 11 changes from the side that had narrowly lost to the All Blacks, but given that Jones had intended for this fixture to replicate their four-day turnaround between the opening two games of their World Cup campaign in Japan next year, it was a performance that will have given him little comfort.
Japan not only completely dominated the first half, both in possession and territory, but also played at the positive rugby, yielding rewards for keeping the ball in hand including turning down three relatively simple kicks at goal. And bringing vim and vigour to their play to prise holes in England's defence.
Once again England's discipline beset their play, conceding eight penalties in the first half alone with Jamie George also being sent to the sin bin. This dominance seemed all the more remarkable given the England had produced the perfect starting, unleashing Cokanisga to make the hard yards before Danny Care finished off well-executed counter-attack.
Yet the rest of the first half was all about Japan. Yu Tamura finally landed a penalty and then centre Nakamura bumped off a soft tackle by Lozowski to score the try to give Japan the lead at Twickenham in the 23rd minute.
Michael Leitch, the New Zealand-born flanker, delivered one of the great back-row performances at the old stadium, carrying, harrying and running and stepping like an outside centre. His first half try left the Twickenham crowd unsure as to whether grimace or applaud, as he bundled his way through four English defenders in an fantastic finish. He almost went over for a second and if he had it, the second half could have been a much closer affair.
England's ability to go back basics finally enabled them to swing the game back in their favour, scoring 25 unanswered points in the second half.
Ford began the fightback with a penalty in the 56th minute and the pressure was eventually lanced when Mark Wilson scored his first international try from an inside pass by Ford after Kyle Sinckler before England's late scoring flourish.
Still, it was Japan who stole the plaudits.