With the result of the tournament already decided, the two teams were playing for pride with Japan hoping to get their first win of the competition.
But Samoa proved too strong again, to win by three wickets in the 43rd over.
Japan's batting continued their improved run to reach 8/135 at the end of their 50 overs.
Former captain Shizuka Miyaji led the way, top scoring with 27, while Etsuko Kobayashi continued her good form with 25.
For Samoa, player of the match Lagi Otila Telea (2/23) was the pick of the bowlers, picking up two wickets.
Japan's score could have been much higher if not for five runouts, most of which were easily avoidable.
Samoa looked to get on top early with some aggressive batting, before a couple of wickets pegged them back.
Lagi Otila Telea was also the star with the bat with a solid 49 while Matile Uliao hit a whirlwind 21.
Appropriately, it was Samoan veteran Perelini Mulitalo who hit the winning runs after announcing that it would be her last game for Samoa after six years.
Japan captain Mai Yanagida had a strong end to her tournament, taking three wickets.
Cricket without Borders had another thrilling match with Papua New Guinea, only to lose by one run for the second time this week. Brenda Tau scored a fantastic 76 for PNG, captain Pauke Siaka took 5/38 and Alice Johnston made 45 for CWOB.
Samoa's win sees them finish second overall at the tournament after PNG wrapped up top spot on Tuesday with their second win over Samoa.
Japan finished third while PNG will now go on to play in the 2017 ICC Women's World Cup Global Qualifier.