You are not permitted to download, save or email this image. Visit image gallery to purchase the image.
The star paceman polled 156 votes to surpass test player of the year Lyon (150) and limited-overs skipper Aaron Finch (146) in Monday night's count.
Alyssa Healy comfortably won the Belinda Clark Award as Australia's top women's cricketer ahead of Megan Schutt and Ashleigh Gardiner.
Allrounder Marcus Stoinis was named men's ODI player of the year and Glenn Maxwell surprisingly won the T20 international award.
Both major awards went to first-time winners, with Steve Smith and David Warner ineligible after a four-year Border Medal stranglehold.
The suspended duo did not attend the black-tie function in Melbourne and only polled a handful of votes in the matches they had played.
Memories of the Cape Town saga were stirred by Cameron Bancroft being voted Australia's second-best player in the same test in which he used sandpaper on the ball.
The opener, also ineligible and not in attendance after a nine-month ban, top-scored with 77 in the first innings.
Cummins claimed maximum votes in Cape Town and the fourth test in Johannesburg, which South Africa won by 492 runs.
"I've obviously had quite a few tough years with injury. I always thought test cricket was the dream but wasn't sure I'd get up there and forge a consistent career," he said.
"Going into last summer and the Ashes, five tests - I'd never done anything like it before so, to get through that, I just had a heap of confidence in my body.
"To do it now, two years in a row, it's been great. I feel like every time I bowl, my rhythm just feels a little bit better."
Monday's count was closely contested, with offspinner Lyon polling top votes in tests in Adelaide, Perth and Abu Dhabi.
Cummins' status as a ODI regular gave him the edge over Lyon, who did not poll in either white-ball format.
Cummins snared 44 wickets at 25.61 across all formats during a 12-month voting period which did not include his recent man-of-the-series performance against Sri Lanka.
The 25-year-old, having climbed to second in the test rankings, will head into the first Ashes test in August on the cusp of reaching 100 test wickets quicker than any other Australian fast bowler since the 19th century.
Healy swept the women's awards, also being named ODI and T20 player of the year, the wicketkeeper-batter rewarded for her T20 World Cup-winning heroics.
Healy was named player of the Caribbean tournament, scoring 225 runs from five innings.
Matthew Wade, still on the outer of Justin Langer's Australian set-up, won men's domestic player of the year.
Will Pucovski and Georgia Wareham were named young players of the year and Dean Jones, Cathryn Fitzpatrick and Billy Murdoch were inducted into the Australian cricket hall of fame.