Tonga led 17-6 at half-time thanks to tries from debutant winger Viliame Lolohea and returning flyer Cooper Vuna on the other flank.
The Kingdom extended their advantage to 28-6 when Penikolo Latu combined defence with attack to score a stunning solo try midway through the second half but a lopsided penalty count ultimately caught up with the 'Ikale Tahi as Sosefo Sakalia, Paula Ngauamo and Sitiveni Mafi were sent to the sin bin in the final quarter of an hour, allowing Samoa to score two consolation tries.
Toutai Kefu said the team's high penalty count is a concern.
