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.