Tonga A had opened the scoring with winger Fetuli Paea's third-minute try, before Samoa A edged ahead when D'Angelo Leiulia converted Ricky Ene's try 10 minutes later. The Tongans responded quickly with another try by their other winger Tuhakavalu Ika to lead 10-7 after 17 minutes but that would be the last points they would score.
Winger Fa'asauvale Lucky and captain Henry Stowers both crossed to give Samoa A a 19-10 lead at half-time and they grabbed control of the match with two tries in six second-half minutes through Ene and hooker Gafa Sua.
The score remained 33-10 until the final minutes when scrum-half Iosua Faalele crossed to claim a bonus-point win that lifts Samoa A into second place in the standings, above Junior Japan on points difference.
"First of all to have a crowd as good as this we are so fortunate. Big up to the Tonga team, they were physical and fast but I thought we stuck to our game plan well. We went wide and had pace and power and were able to finish," said Samoa A captain Henry Stowers.
Samoa A is placed second in the standings.
The Pacific Challenge concludes on Saturday when Fiji Warriors tackle Tonga A and Samoa A meet Junior Japan.