The side lost 3-0 to the hosts at the HFC Bank Stadium in Suva.
17-year-old Jacob Seninawanawa scored Fiji’s opening goal that saw Fiji led 1-0 at the break.
They were also reduced to 10 players after Sailimone Ravonokula was red-carded following a scuffle as tensions flared towards the end of the first half.
But this didn’t stop the Baby Bula Boys from scoring two more goals in the second half through Ibraheem Afazal and William Khan.
However, Tonga will still feature in the quarterfinals against Tahiti at 7pm (Fiji Time) on Saturday.
The match will be held after the first quarterfinal between New Caledonia and Samoa.
The third quarterfinal will be between Fiji and Cook Islands while the last quarterfinal will be between New Zealand and Vanuatu.