Moloney, who finished second in 2009, claimed his first best and fairest with 227 votes. He won the trophy by 26 votes, ahead of defenders Jared Rivers (201) and James Frawley (178), who finished second and third respectively.
Rounding out the top five was ball-winner Nathan Jones (171) and Jack Trengove (170).
The 27-year-old Moloney amassed 509 disposals (23.14 per match) - the best by any Melbourne player in 2011 - and was the club’s standout performer.
Moloney, who has endured his share of injuries in his 130-game AFL career, played all 22 matches in 2011 - the first time he has played every match in a season.
It was the midfielder’s ninth AFL season, after he played 23 matches with Geelong in 2003-04.
Moloney was traded to Melbourne for the 2005 season, and has since played 107 matches, reaching the 100-game milestone this year.
For Rivers, who won the Sid Anderson Memorial Trophy, it was his highest finish to date in a Melbourne best and fairest, and the first time he has claimed a top-three placing.
And after finishing second last year, Frawley backed up with another fine season, claiming the Ron Barassi Snr Memorial Trophy for third.
Jones, who received the Ivor Warne-Smith Memorial Trophy for fourth place, achieved his highest result since coming runner-up in 2007.
And, in just his second AFL season, youngster Jack Trengove claimed the Dick Taylor Memorial Trophy for coming fifth.
Meanwhile, Jordie McKenzie claimed two trophies - the Norm Smith Memorial Trophy (coach’s award) and the Heart and Soul Player Award.
Jack Grimes was presented with the Ron Barassi Jnr Trophy (leadership award), Colin Garland received the Ian Ridley Memorial Trophy (club ambassador award) and Jeremy Howe was awarded the Harold Ball Memorial Trophy (best first year player).
And the Troy Broadbridge Memorial Trophy (highest votegetter by Melbourne-listed player in Casey Scorpions best and fairest) was won by Matthew Bate.
Keith ‘Bluey’ Truscott Memorial Trophy - top 10
Jordie McKenzie (145)