Tonga captain Hemaloto Polovili marked his return from a one match suspension with a well taken low drive from the edge of the box to give his side the lead inside 10 minutes.
The skipper grabbed his second half 30 minutes later as the hosts raced two a 2-0 first half lead.
Samoa did manage to regroup to come out with intent after the break.
Their never-say-die attitude paid dividends in 66th minute when Pago Tunupopo pulled a goal back by netting from close range.
