This was the first time in 24 years the Aussies have won this trophy, with the win made all the more emotional for Day by his losses.
He was supported throughout the tournament, ending Sunday, by his sisters and mother Dening, whose lost close family members in the natural disaster.
Scott and Denmark’s Thomas Bjorn pushed Day on the final day, but the Queenslander was too good.
Scott had made a massive comeback from day one after shooting a shocking opening round of 75 but finished with a five-under 66.
Combined, he and Day ended 17-under, 10 shots ahead of next best US.
“It was great, I really don’t know what to think right now,” Day said.
“All the hard work and dedication I’ve put into my game, especially the last five, 10 years… it’s paying off.
“It’s taken me a while to get my second win and it couldn’t be more fitting with Scotty by my side, winning the World Cup down here in Melbourne.
Both Aussies now shift focus to next week’s Australian Open, but the sombre part of the week wasn’t lost on Day.
“I found out last week we lost those family members in the Philippines, and to have my mum here this week, to see her Saturday morning and to have her here over the weekend and even my sisters and my nephew to be here as a family … is very special,” he said.