Jones won with 365 votes in a remarkably close count, just shading consistent defender Colin Garland who finished on 360 votes.
The two were widely recognised as Melbourne's standout performers in another difficult season for the club and that proved true during the count.
Jones amassed 509 disposals during the 2013 season, at an average of 23.2 per game. The 25-year-old ranked second in the AFL in centre clearances and fifth for clearances.
"To be honest I'm probably more proud this year than I was last year. I was really driven, personally, to back up from last year knowing there'd be more pressure on me due to having a pretty successful year last year," Jones said in his acceptance speech.
"It's been such a dark year for the footy club. Hopefully tonight closes a chapter and we can reopen it in 2014 and get the footy club back to where it belongs.
"I know we are going in the right direction, I know we've got the right people in charge of the footy club and I know that this group will take us where we all want it to be and hopefully that's sooner rather than later."
Jones also had special praise for interim coach Neil Craig, describing him as "the single greatest influence" on his career, to date.
First-year players Dean Terlich (306) and Matt Jones (303) were rewarded for their impressive seasons, placing third and fourth respectively.
Terlich was presented with the Ron Barassi Snr Memorial Trophy, while Jones took out the Ivor-Warne Smith Memorial Trophy.
Colin Sylvia (288) placed fifth in the count and was presented with the Dick Taylor Memorial Trophy.
Nathan Jones capped a memorable night by winning the inaugural James McDonald Trophy as the best club man.
McDonald attended his first Demons function since his unceremonious exit from the club in 2010.
Garland received the Ron Barassi Jnr Trophy (leadership award), Jake Spencer the Norm Smith Memorial Trophy (coaches' award) and Sylvia the Ian Ridley Memorial Trophy (club ambassador award).
Young midfielder Jack Viney was recognised as the best young player, while emerging youngster Jesse Hogan was adjudged best and fairest for VFL affiliate the Casey Scorpions.
Retirees Aaron Davey, David Rodan and Joel Macdonald were also thanked for their contributions on the night.
Davey delivered an emotional and impassioned speech, thanking former teammates James McDonald and Matthew Whelan and describing the Melbourne Football Club as "family".
AWARDS
Keith 'Bluey' Truscott Memorial Trophy: Nathan Jones
Sid Anderson Memorial Trophy: Colin Garland
Ron Barassi Snr Memorial Trophy: Dean Terlich
Ivor-Warne Smith Memorial Trophy: Matt Jones
Dick Taylor Memorial Trophy: Colin Sylvia
James McDonald Trophy (best club man): Nathan Jones
Ron Barassi Jnr Trophy (leadership award): Colin Garland
Ian Ridley Memorial Trophy (club ambassador award): Colin Sylvia
Norm Smith Memorial Trophy (coaches' award): Jake Spencer
Harold Ball Memorial Trophy (best young player): Jack Viney
Troy Broadbridge Memorial Trophy (Casey Scorpions best and fairest): Jesse Hogan
TOP 10
1 – Nathan Jones (365)
2 – Colin Garland (360)
3 – Dean Terlich (306)
4 – Matt Jones (303)
5 – Colin Sylvia (288)
6 – Lynden Dunn (270)
7 – James Frawley (268)
8 – Jack Trengove (257)
9 – Jeremy Howe (256)
10 – Tom McDonald (249)
Twitter: @AFL_BenGuthrie
