RNZ reports both teams were playing for pride in Apia after Papua New Guinea sealed top spot a day earlier.
Shizuka Miyaji top-scored with 27 as Japan posted their best total of the week, reaching 135 for 8 from 50 overs.
Lagi Otila Telea was the pick of the bowlers for the home side with 2 for 23, while the hosts also managed to execute a whopping five run-outs.
