The combined results left Samoa, American Samoa and Cook Islands all level on six points after three matches, with Samoa winning the group on goal difference.
They finished at plus three, with American Samoa and Cook Island at plus two.
As group winners, Samoa progressed to the 2016 Oceania Nations Cup, joining New Zealand, Fiji, Solomon Islands, Vanuatu, Tahiti, New Caledonia and Papua New Guinea in the eight-nation tournament.
Six of those eight teams will continue to the third round of World Cup qualifiers while four will advance to the Oceania Nations Cup semi-finals, which will decide the region's representative at the 2017 Confederations Cup.
John Hall, playing just his third international, scored twice for Samoa against hosts Tonga to give his team the crucial superior goal difference after Andrew Mobberley opened the scoring after just nine minutes.
Cook Islands held America Samoa scoreless for almost an hour before giving up two quick goals and they were unable to get one back even when American Samoa were down a man for the last 10 minutes when Ryan Samuelu was sent off following a second booking.
(Writing by Julian Linden in Singapore; editing by Amlan Chakraborty)
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