Johnathan Sesejack scored the opener in the 18th minute while Patrick Joseph found the equaliser for the Marika Rodu-coached side in the 22nd minute from the penalty spot.
In the 47th minute, Claude Aru scored the winner from a beautiful free-kick just from outside the penalty box.
Fiji also lost 1-4 to the Solomon Islands earlier on.
The Bula Boys will face the Junior Bula Boys while Vanuatu will take on the Solomon Islands on Thursday in the second match at Churchill Park in Lautoka.
