The tournament, which also involves Fiji, doubles as a qualifier for the World Cup with the combined 2016 and 2017 results deciding which two teams from the region win automatic berths in Japan in 2019.
It was the first test Tonga have hosted in eight years and drew a crowd of around 10,000 at the newly-refurbished Teufaiva Stadium in the Tongan capital.
Tongan halfback Sonatane Takulua scored all of his side's points in the second half with a converted try and a penalty as they built on their 20-16 lead at the break to hold off a late charge from the Samoans.
The victory allowed Tonga to draw level with Samoa on five points in the combined standings from the two campaigns ahead of their meeting with Fiji in Suva next weekend.
Fiji top the table on eight points after winning both of their matches last year and are in the driving seat to qualify as "Oceania 1" and join Australia, Wales and Georgia in Pool D at the World Cup.
The country that finishes second, "Oceania 2", will go into the toughest pool in the tournament along with England, France and Argentina.
The third placed Oceania team will go into a playoff against a second tier European team for a spot in Pool A with Ireland, Scotland and hosts Japan.
Samoa host Fiji in Apia in the final match of the tournament on July 15
Photo: Photosport Tongan rugby team celebrate