Manly halfback Daly Cherry-Evans finished third, with his teammate, Tom Trbojevic, fourth despite missing large parts of the season.
Roosters second-rower Olivia Kernick won the women’s Dally M, taking her first major prize by finishing two points clear of Parramatta fullback Abbi Church and Gold Coast halfback Lauren Brown.
Hughes’ maiden top gong comes after what has clearly been the best year of his career to date.
The Storm No.7 stepped up in the absence of Cameron Munster through the middle stage of the season and helped take Melbourne to the grand final.
“I don’t really play the game for individual accolades, I play it for team accolades,” Hughes said.
“That was the way I was looking at it coming into it.
“But now I have been lucky enough to win it, I see how special it is. When you see the players who have won it, it’s pretty crazy.”
His showdown with Penrith halfback Nathan Cleary also looms as a heavyweight battle in Sunday’s decider.
If Hughes wins out in that, he can become just the eighth player in history to win a premiership and Dally M in the same year.
“That’s the next job,” Hughes said.
“We’re in a grand final, and now it’s time to prepare for that.
“It would be awesome to get the double, but just winning a premiership with my Storm teammates this year is a dream.”
Wednesday night’s coveted honour at Royal Randwick is a fitting reward for Hughes after a superb season.
Hughes’ triumph came on a big night for the Storm with Craig Bellamy named coach of the year.
Harry Grant was named hooker of the year, Katoa one of the second-rowers of the year (Angus Crichton is the other) and Xavier Coates handed the try-of-the-year award.
Penrith had two players in the team of the year, while Canterbury’s Stephen Crichton was named captain and in the centres.
Hughes had started the night down in equal-15th spot and 16 points behind leader Dylan Edwards when votes went behind closed doors after round 12.
But with six points also deducted from a suspension, he stormed home with 45 points out of a possible 69 from his final 12 games.
In doing so, the prize caps a stunning turnaround for the 29-year-old, who spent the early parts of his career bouncing around clubs.
He is the first New Zealand No.7 to win the NRL’s major award since Freeman in 1992 and only the fourth Kiwi in history to claim it from any position.
Meanwhile, Dolphins winger Jack Bostock claimed the men’s rookie of the year and Kasey Reh the women’s.
Brisbane’s Scott Prince was named NRLW coach of the year, while Cronulla leader Tiana Penitani was best captain.
MEN’S DALLY M LEADERBOARD
Jahrome Hughes - 62
James Tedesco - 61
Daly Cherry-Evans - 51
Tom Trbojevic - 46
Scott Drinkwater - 45
Team of the year: James Tedesco, Zac Lomax, Stephen Crichton (capt), Herbie Farnworth, Brian To’o, Tom Dearden, Jahrome Hughes, Joseph Tapine, Harry Grant, Addin Fonua-Blake, Angus Crichton, Elisa Katoa, Isaah Yeo. Coach: Craig Bellamy. Rookie: Jack Bostock.
WOMEN’S DALLY M LEADERBOARD
Olivia Kernick - 22
Abbi Church - 20
Lauren Brown - 20
Tamika Upton - 19
Julia Robinson, Simaima Taufa, Yasmin Clydsdale - 17
Team of the year: Abbi Church, Julia Robinson, Isabelle Kelly, Tiana Penitani (capt), Stacey Wacka, Zahara Tamara, Lauren Brown, Shannon Mato, Keeley Davis, Millie Elliott, Olivia Kernick, Yasmin Clydsdale, Simaima Taufa. Coach: Scott Prince. Rookie: Kasey Reh.