Morrison's coalition defied forecasts to be re-elected on Saturday in what he called a political miracle.
The Coalition won 74 seats in the House of Representatives of a possible 151, with 5 electorates still in doubt, meaning it could still attain the 76 required to form a majority government.
With the defeat, Mr Shorten has stepped down as the Labor leader, but not before using his concession speech to criticise Coalition preference deals with the United Australia Party and Pauline Hanson's One Nation which he says, "hurt out vote in a lot of places where it mattered most, particularly in Queensland and NSW".
The AEC said the coalition is ahead in one of the three seats that have not been declared.
Polls had shown the government trailing the opposition for the past two years and exit polls had suggested a Labor win for the first time in six years.
Morrison had become Australia's sixth prime minister in only eight years.
On Sunday Anthony Albanese announced his intention to run as a candidate for leader, saying he believed he was the best person to lead the party back into government.
In his victory speech, the continuing Prime Minister said that "Tonight is not about me, it's not even about the Liberal Party".
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He said the US' decision to counter possible threats gave the "Iranians time to recalculate". Several tankers in the Gulf, including two Saudi vessels, were reportedly sabotaged as well.
Most late surveys showed Labor leader Bill Shorten as having a small but clear lead over Morrison as preferred prime minister, with 51 percent to 49 percent. "If he replaces them with people who have argued for stronger action, it will be marker".
Labor has so far secured enough backing to get only 65 seats.
Tanya Plibersek, Shorten's deputy, said she was considering running for the leadership.
Meanwhile his guest, ABC presenter Patricia Karvelas described Labor's policy agenda as an incoherent "shopping list".
While the prime minister was rarely flanked by his minister during the election campaign, he now he faces the task of deciding who will form his refreshed ministry and cabinet.
One telling result came on Monday, when high-profile independent lawmaker Dr. Kerryn Phelps conceded defeat to the Liberal Party in the Sydney electorate of Wentworth - the seat vacated by Turnbull on his resignation from Parliament past year.
Shorten, a 52-year-old former labor union leader, has also promised a range of reforms, including the government paying all of a patients' costs for cancer treatment and a reduction of tax breaks for landlords.
The other high-profile independent candidate of the election, Kerryn Phelps, on Monday morning conceded defeat to Dave Sharma in Wentworth.
"Clearly the country decided it wanted to return a Liberal government", P helps told reporters.