Almost three-quarters of the electorate voted on Saturday on whether divorce should be introduced in Malta.
A majority Catholic country, Malta is the only EU country not to allow divorce.
Figures from the electoral commission late on Saturday showed turnout was 72%, the Times of Malta reports.
“Even though the result is not what I wished for, now it is our duty to see that the will of the majority is respected,” Dr Gonzi said in a televised speech.
Dr Gonzi, who campaigned against the introduction of divorce, has said it is now up the parliament to enact a law legalising the dissolution of marriage on the island.
The Catholic Church, which is very influential in the archipelago, had also supported a “No” vote during the campaign.
Malta’s history has begun a new chapter after its citizens voted to introduce divorce to the island.