Japan, sent into bat, scored 161 off 48 overs with opening batsmen Tetsuro Chino topscoring with 51 off 120 balls and Cooks wicket-keeper Ioane Tangimetua claiming five catches.
The Cook Islands fell just short, dismissed for 155 with Tuakana Marukore topscoring with 55 and Chris Brown chipping in with 45.
Japanese paceman Patrick Giles-Jones finished with 3-31 off 10 overs.
Japan and the Cook Islands, by finishing first and second, qualified for the EAP Cricket Trophy to be played in mid-2006 to claim a place in the World Cricket League in early 2007.
Final placings in EAP Cricket Cup - 1 Japan, 2 Cook Islands, 3 Vanuatu, 4 Tonga, 5 Indonesia, 6 Samoa.