The Etienne Mermer-coached side needed only a draw to advance to the semi-finals and looked on course to complete that task when Petch Ham put them ahead with a 49th-minute headed goal.
But Haiti levelled in the 67th minute courtesy of midfielder Gedeon and their place in the semi-finals was confirmed when the unmarked Jean Bonhomme rifled home the winner at the far post with only minutes remaining.
Vanuatu now join fellow Oceania representatives Papua New Guinea, whose U-15 women’s team lost to 4-0 to Turkey on Wednesday, in bowing out of medal contention at the tournament.
Haiti, who were thrashed 9-0 by Bolivia in their first match, leapfrog Vanuatu into second place and will meet Singapore in the semi-finals, while Mermer’s young charges must make do with a fifth place playoff against Zimbabwe.
In the day’s other match, Singapore defeated ten-man Montenegro 3-2 to secure top spot in Group D in front of a raucous crowd of 5,850 fans.
Montenegro, who had been tipped as favourites for the gold medal, now face a tricky semi-final with the in-form Bolivia.
Results
Vanuatu 1-2 Haiti
Singapore 3-2 Montenegro
Semi Finals
Sunday 22 August
Singapore vs Haiti
Montenegro vs Bolivia
Mens’ 5th Place playoff
Monday 23 August
Vanuatu vs Zimbabwe
Womens’ 5th Place playoff
Monday 23 August
Papua New Guinea vs Trinidad and Tobago