With 99.11% of the ballots counted, 66.25% of the voters said "yes" to Croatia's EU accession, while 33.15% voted against.
The turnout to the referendum remained low, with just 43.67% of the 1,955,326 voters going to the ballot box.
Eurosceptics were visibly disappointed by the result and stressed it was "shameful" that so few people decided the fate of the whole country. Opponents to Croatia’s accession had warned that the EU was not a representative democracy, but a "bureaucratic fortress" in which the country would lose its sovereignty and national identity.
The country's leaders gathered in the Parliament after closing the polls and began to receive distinguished guests, ambassadors, trade union representatives, former ministers and many others who wanted the new government to celebrate the historic decision.
Croatian President Ivo Josipović said the voters’ decision determined Croatia's European future. He also thanked those who voted against, saying that their doubts and anxieties also need to be taken into account.
"This is a turning point in Croatia's history," said Prime Minister Zoran Milanović. Milanović, a former diplomat, won the December elections as leader of Kukuriku ("cock-a-doodle-doo") in Croatian, a centre-left coalition that defeated the centre-right HDZ party of former Prime Minister Jadranka Kosor.
"Never again someone else will decide our fate," Kosor was quoted as saying.
Croatia is bound to become the second former Yugoslav republic to join the Union, after Slovenia joined in May 2004. The country fought a fratricidal war with Serbia between 1991 and 1995. In the former Yugoslavia, many Croats felt that Serbs had the last word in running the country.
In recent days, opponents organised mass rallies and warned that Croatia would surrender its national sovereignty to the Brussels bureaucracy. However, according to surveys, the support for accession remained high in the days prior to the vote.
Foreign Affairs Minister Vesna Pusić, commenting on the turnout, said the country had a tradition of low participation in elections.