The top pairing of Miller Pata and Sherysyn Toko were beaten in three sets by Japan's Akiko Hasegawa and Azusa Futami 19-21, 21-19, 7-15.
Meanwhile Vanuatu's second team of Loti Joe and Majabelle Lawac went down in straight sets, 10-21, 17-21, against Chiyo Suzuki and Yurika Sakaguch.
The result bring an end to Vanautu's Tokyo 2020 qualification journey, while Japan advance to the final four in the women's draw, with the winner securing the final berth at next month's Summer Games.
