Just 1.5 percent of the votes cast were for independence for the Caribbean island, and just 1.3 percent of those who cast valid ballots opted for maintaining Puerto Rico's current status as a United States commonwealth.
But the ballot's previous language prompted calls by opposition parties to boycott what they saw as a rigged vote.
"I hope after 100 years of being a territory of the United States, we can send a message to Congress in the U.S. that Puerto Rico is ready to do something with its future", said Marco Rodriguez, a voter in Guaynabo.
As U.S. citizens, Puerto Ricans can simply pack up and move to the mainland U.S. for better job and educational opportunities.
Statehood's advocates say it would help the economy; its opponents warn that the island will lose its cultural identity and struggle even more financially because it will suddenly have to pay millions of dollars in federal taxes.
Hector Ferrer, leader of Popular Democratic Party, said eight out of 10 "stayed home" or "went to the beach" instead of voting.
This year's referendum coincides with the 100th anniversary of the United States granting US citizenship to Puerto Ricans, though they are barred from voting in presidential elections and have only one congressional representative with limited voting powers. Congress laid out a process through a provision in a 2014 law that said that if Puerto Rico wanted the federal government to pay attention to another status referendum, it had to follow certain rules.
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With 97 percent of the vote counted, a total of 97.17 percent of the Puerto Ricans who turned out to vote in Sunday's plebiscite on the island's legal status opted for US statehood. In a similar referendum in 2012, before the island's financial troubles deepened, 61% voted for statehood.
Despite the low level of participation, Puerto Rican Governor Ricardo Rossello vowed, after casting his vote for full annexation by the United States, to defend internationally the result.
Those who remain behind have faced new taxes and higher utility bills on an island where food is 22 percent more expensive than the US mainland and public services are 64 percent more expensive.
Only Congress can make Puerto Rico a state, and there's little appetite to do that right now.
The Republican Party has traditionally supported statehood for Puerto Rico, while the Democratic Party said it was ready to support whatever decision Puerto Ricans made through fair, open and democratic elections.
JUAN GONZÁLEZ: Yes, it's actually probably the poorest showing that the pro-statehood party has had in about 50 years, because so few people voted.
Puerto Rico has suffered its worst economic recession in decades and its outstanding bond debt has climbed to over $70 billion.
Sunday's two-part plebiscite, the fifth held since 1967, will decide the future of the unincorporated USA territory.