Samoa edged the game 24-22 in Sapporo in what was a dress rehearsal for the two teams’ Pool D encounter at the World Cup in France later this year.
Japan took an early lead, but suffered a blow when former captain Leitch was red-carded 10 minutes before the break for a dangerous tackle on Samoa’s So’otala Fa’aso’o.
Japan flank Kazuki Himeno said it was “disappointing” that the Brave Blossoms could not shake off the mental effects of Leitch’s dismissal.
“We wanted to keep going without being too pessimistic about it but it did put a damper on our team’s morale,” he said.
“We couldn’t turn the tide.”
The New Zealand-born Leitch was playing in the city where he first lived after arriving in Japan as a 15-year-old.
But his involvement did not even last until half-time after he saw red for hitting Fa’aso’o high in the tackle.
Japan flyhalf Lee Seung-sin tried to take the positives out of playing with 14 men.
“How we play with a man down isn’t something we can experience in training,” he said.
“We did everything we could in that situation and we did lose in the end, but it was a positive experience and in a sense we learned a lot.”
Japan and Samoa have been drawn together in Pool D at the World Cup alongside England, Argentina and Chile.
They face each other in Toulouse on September 28.
Japan staked an early lead after a try from debutant Amato Fakatava, who wriggled over the line in the sixth minute.
Samoa, who handed a debut to former Wallabies playmaker Christian Leali’ifano, came back into the match with tries from Alamanda Motuga and Jonathan Taumateine.
Japan stayed ahead through flyhalf Lee’s boot, but another try from Samoa’s Tumua Manu in the 63rd minute turned the tables on the Brave Blossoms.
Japan reached the World Cup quarterfinals for the first time on home soil four years ago, and Leitch has said he believes they can win this year’s tournament.
Fullback Ryohei Yamanaka admitted that they had “challenges to overcome” if they are to make an impact.
“We want to prepare well,” he said.
“We will fix the problems from today’s game so that we can produce good results at the World Cup.”
Japan continue their preparations with another home Test match against Tonga next Saturday, before playing Fiji one week later.