Political newcomer Robert Abela is set to take over from Joseph Muscat following Saturday's vote.
Election results, which was revealed on Sunday, handed the leader of the ruling Labour Party 58 per cent of the votes.
He defeated initial favourite - deputy prime minister and minister of health Chris Fearne.
"I am humbled," Abela told supporters. "I thank my friend Chris (Fearne) and look forward to working together for the good of the party and the country. There is only one winner today, the Labour Party."
Abela, who was elected to the parliament for the first time just over two years ago, has promised to place increased government focus on social issues and affordable housing.
Muscat, who announced his resignation on December 1, has been accused of protecting associates involved in the 2017 murder of journalist Daphne Caruana Galizia.
Israeli troops and tanks pushed on Saturday into parts of a congested northern Gaza Strip district that they had previously skirted in the more than seven-month-old war, killing and wounding dozens of Palestinians, medics and residents said.
Slovak Prime Minister Robert Fico is no longer in immediate danger but still in a serious condition, his deputy said on Sunday, four days after an assassination attempt that sent shockwaves through Europe.
At least 47 people have died after continued heavy rain and flooding in northern Afghanistan, an official said on Sunday, a day after a similar number were killed in a central province.
Russian airstrikes killed at least ten people and injured many others in a recreation area just outside Ukraine's northeastern city of Kharkiv on Sunday, local officials said.