Despite being down in the opinion polls, his Liberal-National coalition had won 74 of the 76 seats needed to form a majority government. It went into the election as a minority government, with just 73 seats.
His rival, Bill Shorten stood down on Saturday night following the defeat.
Speaking after his victory, he told supporters: "I've always believed in miracles."
"I give thanks to live in the greatest country in all the world. Thanks again to all Australians all across the country."
Morrison worshipped at Horizon Church in Sydney before attending a local football game.
During the election campaign his conservative views on homosexuality were used against him by rivals and media.
Morrison was named Australia's 30th Prime Minister last year. He'll now serve a three year term.
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