Van der Walt and Lemeki extended the lead to 23-0 within 10 minutes of restarting and when replacement Kazuki Himeno crossed in the 68th minute the home side had sewn up the match.
Neither team adjusted to the wet weather very well with numerous handling errors and the rain forced both sides into a tactical kicking battle.
The visitors were not helped by having flanker Viktor Koelishvili sinbinned midway through the first half, but Japan were not able to hammer home their extra man advantage.
Jamie Joseph's side have shown some impressive consistency against European opposition in their three tests this month as they prepare to host next year's Rugby World Cup.
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They shared a two-match series with Italy after they recorded a 34-17 win in the first test in Oita before losing 25-22 in the second in Kobe last week.
Georgia snuck to a 16-15 victory over Tonga in the Pacific nations cup but were then hammered 37-15 by Fiji in what was essentially the final of the tournament last week.
(Reporting by Greg Stutchbury in Wellington; Editing by Amlan Chakraborty)
