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.
Hamas handed over three Israeli hostages on Saturday, whose emaciated appearance shocked Israelis following their release on live TV, in the latest stage of a ceasefire deal aimed at ending the 15-month war in Gaza.
The US Coast Guard in Alaska found the wreckage of a small plane atop frozen sea ice on Friday, after the aircraft suddenly lost altitude on Thursday and the crash killed all 10 people on board, officials said.
A US judge has temporarily allowed roughly 2,700 US Agency for International Development employees put on leave by President Donald Trump's administration to go back to work, pausing aspects of a plan to dismantle the agency.
Hamas accused Israel of multiple breaches of their ceasefire agreement on Friday, a day before the scheduled exchange of three more Israeli hostages for Palestinian prisoners in the latest stage in a fragile deal aimed at ending the war in Gaza.