A great result for the champion team who last won the title 28 years ago at the 1991 Pacific Games in Port Moresby.
Although the Tongan side looked strong from the outset and led for the majority of the first three quarters, it was the Cook Islands who dug deep in the final quarter to take the win by one.
A lob to 188cm Tongan shooter Uneeq Palavi in the dying seconds was later disallowed after the final whistle had been drowned out by the cheers of the Cook Islands and Tongan fans in the crowd.
Taking silver back to the Kingdom of Tonga is a first for the side that have placed third and fifth in previous years.
Earlier, Papua New Guinea were awarded bronze after a comfortable win over host team Samoa, 64 to 35.
Nearby nations Solomon Islands, Norfolk Islands, American Samoa, Niue and Tokelau also travelled to the Samoan capital to take part in the 16th edition of the tournament but were ruled out in the preliminary rounds.
Netball Samoa CEO Rosemarie Esera was thrilled to have welcomed neighbouring nations to compete in a tournament that helps to build the profile of netball in the Pacific.
“The games have been a great opportunity to educate and expose our players to the high-performance environment,” said Esera.
Teams will now look to begin preparations to qualify for the 2021 Netball Youth World Cup in Fiji.