The hosts were pumped up with the two early goals and kept the Japanese defence under sustained pressure. Stephen Jenness, playing in his 100th international, made the scoreline 3-0 as the home side was sitting pretty at half-time.
The black brigade pressed home the advantage when Hugo Inglis scored his second of the day. Stephen Jenness also got his name in the scoresheet for the second time when he made the most of a Hugo Inglis baseline cross.
Japan captain Koji Kayukawa pulled one back in the 59th minute, but there was never any doubt as to which team reigned supreme on the pitch.
Earlier, New Zealand won the second Test 2-0 after drawing the opening tie 2-2.