Unable to attend after his horror ankle injury in Penrith's preliminary final loss, Cleary accepted Wednesday night's award from his couch.
The Panthers champion finished 14 points clear of Cronulla half Braydon Trindall, who was in the hunt until a dislocated shoulder ended his regular season.
Tamika Upton also claimed her third Dally M Medal as NRLW player of the year, defending her crown from last year when the Brisbane fullback became the award's first multiple winner.
Warriors mentor Andrew Webster pipped Justin Holbrook to be the NRL's coach of the year with finals not counted, while Canberra playmaker Ethan Sanders was rookie of the year.
But the story of the night was Cleary, who left hospital on Wednesday after undergoing emergency surgery on his ankle.
Despite being the best player of this decade, the Dally M had somehow evaded Cleary due to a run of injuries or suspensions.
But he played 23 games this year, setting up 29 tries and acting as the chief architect of Penrith's run to a preliminary final.
Cleary led the race for the majority of the year, polling 67 votes ahead of Trindall's 53 and Panther Dylan Edwards' 52.
"I can't thank everyone enough for the messages they've sent through and the support I've felt," Cleary said.
"In terms of being able to win the Dally M award, I'm super grateful for that as well.
"I want to start off by thanking all my teammates. None of this would be possible without them. They definitely made me 10,000 times the player that I am."
Cleary had earlier this year claimed his maiden Wally Lewis Medal, silencing his critics by leading NSW to a 2-1 State of Origin series victory.
The 28-year-old has also won two Clive Churchill Medals to go with his four premierships at Penrith.
Meanwhile, Newcastle's magical run to the grand final was not reflected in the Dally M team of the year, with the Knights having no players in the side.
Kalyn Ponga also missed out on captain of the year and Holbrook as coach, with all voting complete at the end of the regular season, when the Knights finished seventh.
Robert Toia and Naufahu Whyte were the two Sydney Roosters representatives named in the side.
In the NRLW, Upton's win came after she polled six points in the penultimate round and then one point in Round 11 to beat Wests Tigers' half Raecene McGregor.
The Broncos No.1 is now the clear best player in the women's game over the opening eight years of the NRLW.
"I've still got lots to improve on," Upton said, with Sunday's grand final against Sydney Roosters still looming.
"We've seen that this year. I have been learning being a sole captain this year.
"We went through a tricky patch this year and I learnt a lot about myself as an individual, but a footy player as well."
Newcastle winger Mercedez Taulelei-Siala was named rookie of the year, after a season when she scored 13 tries in 12 games. Gold Coast mentor Karyn Murphy won the coach's medal.
The heart-touching moment of the night came when South Sydney's Jai Arrow was presented the Peter Frilingos headline moment and the Provan-Summons spirit of the game award for the way he has approached his battle with motor neurone disease.
NRL TEAM OF THE YEAR:
Dylan Edwards, Thomas Jenkins, Herbie Farnworth, Robert Toia, Selwyn Cobbo, Braydon Trindall, Nathan Cleary, James Fisher-Harris, Wayde Egan, Naufahu Whyte, Haumole Olakau'atu, Hamish Stewart, Erin Clark. Coach: Andrew Webster.
NRLW TEAM OF THE YEAR
Tamika Upton, Julia Robinson, Isabelle Kelly, Jess Sergis, Brydie Parker, Teagan Levi, Raecene McGregor, Millie Elliott, Keeley Nizza, Sarah Togatuki, Evania Isa'ako, Shaylee Bent, Olivia Kernick. Coach: Karyn Murphy.
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