Piers, who recently signed with Sky News, flew into Australia with media tycoon Lachlan Murdoch on Monday night.
The former Good Morning Britain presenter hadn't been announced as a guest host but had taken Karl's seat at around 7:35am.
Piers kicked off his time on the show by reading the weather, saying, "G'day, Australia. Let's start with the weather forecast. Contrary to everything that every Australian has ever told me about the weather in Sydney, it's raining.
"And, in fact, it's been raining every minute since I got to Australia and it's going to rain every minute for the rest of the week I'm spending in Australia."
Piers then made fun of Karl, who'd been relegated to a nearby couch while his chair was taken.
"But the good news for Ally is that she's finally got someone next to her who is intelligent, handsome, younger, [has a] better accent and a proven track record of smashing ratings records on breakfast television," Piers said as Karl was seen jokingly looking upset.
The host admitted he felt right at home next to Ally in Karl's seat, "You know what, Ally? I like it here. This feels natural to me.
"Karl who? That's showbiz. [He] made the fatal strategic error of letting me sit in his chair. And it just immediately feels natural."
He then added to Ally, "You look happier. You look like you've come alive!"
"I didn't know what joy was for the last two years," she joked.
"You know what, it feels right, this chemistry, immediately - bouncing off each other," he added, with Ally responding that he was just like Karl, because he didn't let her get a word in.
Karl jokingly gave Piers a huge thumbs up and said, "Love you, Piers!"
While Karl and Ally loved having Piers on the show, fans took to social media to say they'd be switching off after seeing the controversial presenter on Today.
"We switch off your program when you try and promote this person and his opinions," one Twitter user said.
"Why are you promoting this person and his views? No interest in him," another added.
"F off back to England, Piers," a third wrote.
"So sad to see Channel 9 promoting this idiot," someone else added.
"Nothing says change the channel more than 'Up next Piers Morgan'," another joked.
Others were more supportive with one user writing, "I always like Piers Morgan."
Piers famously walked off Good Morning Britain after being questioned over his Meghan Markle views after his co-host Alex Beresford condemned his constant 'trashing' of the Duchess, particularly after her bombshell interview with Oprah Winfrey.
At the time, he copped backlash for suggesting Meghan's statement that she 'didn't want to live anymore' was false, as well as for years of ranting about the Duchess on TV.
"I don’t believe a word she says," he said of the interview.
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