Smith, on for Ford in the 57th minute, added urgency to England's play. Fisilau made a heavy defensive hit and later scored, taking a direct route to the line.
The 24-year-old, asked to supply the pace and power lost to Immanuel Feyi-Waboso's injury, scored in the opening minute and set the tone for a match decided early.
England have targeted fast starts this autumn. They tore into Japan from the outset and kept the pressure on long after the result was beyond doubt.
Three defenders were left on the ground as Joseph finished that first try. Genge then scored in the same direct style, making England's intent plain.
That approach wavered only briefly, when England were awarded an early penalty in front of the posts.
The lead was 32-3 inside 20 minutes. Ben Earl finished a driving maul to make it 49-10 at the break.
Even without some first-choice players, England attacked with speed and purpose. Japan had no answer as the half wore on.
Japan could not find the quick rucks and sharp passing that have troubled the game's major powers in the past. They were badly over-matched.
A side that could not cope with England at full strength faded further as the evening went on.
Forward power was the clearest edge. Martin forced his way over from close range early in the second half.
With the outcome long settled, attention turned to players trying to press their claims alongside Joseph.
Joseph's five tries came four years after he won his first cap as a teenager, entering as a late replacement against Australia.
One-sided afternoons are not unknown on this ground. Few recent ones have been this complete.
England came into the autumn as underdogs for this year's rematch. Performances this weekend, including the win over Japan, suggest those odds are narrowing, and may be turning toward the hosts.