In a tight contest at the Teufaiva Sport Stadium in Nuku’alofa, Ben Volavola kicked three penalties while Leone Nakarawa got an important try to seal the win for Fiji.
Both sides were locked at 3-all at half-time, according to Fiji Village.
Tonga took the lead early in the second half after Siegfried Fisiihoi crossed over Fiji’s tryline.
It took Fiji only two minutes to respond and Nakarawa scored Fiji’s only try in the 48th minute.
Fiji will be pooled with Australia, Wales and Georgia in the 2019 Rugby World Cup.