Niemann cashed in with an eagle at the second extra hole after a trio of big-name local hopes let the famous trophy slip during a wild final round in Sydney.
Starting the day four shots behind, Niemann - who plies his trade on Greg Norman's Saudi-backed breakaway league after defecting from the PGA Tour - stormed home with a final-round five-under-par 66.
Hoshino closed with a 70 to make the playoff at 14 under but wound up second for the second Sunday running, having last week finished three shots behind emerging Australian superstar Min Woo Loo at the Australian PGA.
Lee will be ruing not saluting again after he entered the final round as co-leader with Hoshino and in the form of his life.
And former world No.1 Adam Scott and fellow US PGA Tour star Lucas Herbert also had one hand on the Stonehaven Cup during Sunday's last round.
But all three fan favourites suffered heartbreak, as did Lee's superstar sister Minjee, who had to settle for the runner-up prize in the women's Open after South African Ashleigh Buhai defended her title with a thrilling one-shot win.
While Lee relinquished his lead early, Scott and Herbert had turns at looking likely winners down the stretch, only to falter in incredible fashion.
In the space of seven depressing minutes for Australian golf fans, both suffered triple-bogey sevens to see their hopes vanish.
From 14 under and outright leader with three holes to play, Scott - who started his round on the 10th - drove out of bounds on the par-4 seventh.
After making the long walk back to the tee, he couldn't make par with his second ball and suddenly tumbled to 11 under.
"I think if it was the last hole, I might have stormed off," Scott said after adding his tie for fourth - three shots out of the playoff - to a trio of runner-up finishes since winning the Open for the only time in 2009.
Moments after Scott's mishap, Herbert, also at 14 under, found the trees on the ninth and recorded his own gut-wrenching triple-bogey. He never recovered.
"It was super frustrating because you'd hit decent shots and get punished," Herbert said of the gruelling last-day conditions.
"I didn't do a lot wrong. I missed a short putt, I blinked and made triple. It's hard to see your name fall out of the lead like that."
As much as Scott's and Herbert's crashes hurt, Lee will likely rue the one that got away most.
Bidding to join an elite group of only six players, including legends Greg Norman (1985), Peter Thomson (1967) and Kel Nagel (1959) to have completed the Australian PGA and Open double, the 25-year-old may never have a better chance.
But the West Australian was philosophical about falling two shots short of at least making the playoff with his closing 72.
"The putts didn't go my way and I didn't hit it well enough," Lee said.
"I was up and down from literally everywhere. It's not good enough to win a tournament.
"But it's been a good year and I'm pretty proud of the way I've finished."
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