The host of The Voice, Dancing with the Stars and Big Brother on the Seven network beat favourite Hamish Blake, who had been expected to take out his third Gold.
"I cannot believe that, I'm not used to being on TV," Kruger joked as she accepted the award.
Another big winner has been comedy show Colin from Accounts by husband-and-wife team Patrick Brammall and Harriet Dyer, which has won three Logies.
The series has won most outstanding comedy, while most outstanding actress has gone to Dyer and to Brammall, most outstanding actor.
Brammall thanked everyone behind the show as well as his fellow nominees.
"You're all outstanding as far as I'm concerned, but not as outstanding as me," he joked.
The awards are being held in Sydney for the first time in 37 years, with comedian Sam Pang the first solo Logies host in more than a decade, delivering one zinger after another.
"Welcome to the Logies... over the next two days we're going to have a lot of fun," he said.
"If you're under 25, welcome to free-to-air television."
Most popular actor went to Sam Neill for his role on The Twelve, and the film star said he was gobsmacked.
"There's so many actors in the show I'm not even sure I was the main actor," he said.
In a controversial win, well-known performer Amy Shark took home most popular new talent for her role on Australian Idol.
Most popular actress went to Kitty Flanagan for her role on Fisk, with the acceptance speech delivered by co-star and fellow nominee Julia Zemiro, who had to thank herself.
The Bert Newton award for most popular presenter went to Tony Armstrong, last year's winner of most popular new talent, who once again flagged contract renegotiations on the back of the win.
"Mate, my agents are calling tomorrow," he told his boss in the audience.
Home and Away won most popular drama while Heartbreak High's Thomas Weatherall was named most outstanding supporting actor.
Most outstanding reality show went to Australian Survivor: Heroes vs Villains, and in a message from Samoa, host Jonathan LaPaglia thanked those who voted for the show.
"I guess you could say the tribe has spoken," he said.
Most outstanding children's program went to ABC's Crazy Fun Park, beating global juggernaut Bluey, and the audience-voted most popular comedy award went to Have You Been Paying Attention?
Todd McKenney hit the stage with an unexpected cabaret number dedicated to reality television and its low production costs, before awarding most popular reality program to MasterChef Australia.
The MasterChef team dedicated the award to host Jock Zonfrillo, who died in April.
"Big man, this is 100 per cent dedicated to you," producer Marty Benson said.
The television executive who made Neighbours a global success, Brian Walsh, was posthumously inducted into the Logies Hall of Fame.
There were tributes to Barry Humphries and Olivia Newton John, followed by a rendition of Xanadu by Kate Miller-Heidke.
Lightening the mood, Pang presented his own in memoriam to television programs that have been axed, including The Real Love Boat and Rush.
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