Rockliff polled 37.5 votes to hold out three-time champion Simon Black (35.5) and good mate Jack Redden (35) in a tight count at the Brisbane Convention and Exhibition Centre.
The 21-year-old became the youngest ever Lions' club champion on the back of a storming second half of the season.
It came just 12 months after he was named the 2010 Rookie of the Year.
After 11 rounds Rockliff was outside the top 10 following two weeks on the sideline with a calf strain, but an irresistible home stretch earned the vice-captain the coveted award named in honour of Lions' legends Kevin Murray and Roger Merrett.
He averaged 30 disposals a game in the final nine rounds and more than 27 a game over the season.
Rockliff was humbled by the award that saw him join the likes of Michael Voss, Jason Akermanis, Jonathan Brown and Black as past winners.
"I'm speechless. It doesn't sit comfortably with me sitting in that category of blokes that have won it in the past," Rockliff said.
"I still have a lot of work to do to be mentioned in the same sentence as the blokes. I don't play for individual awards, I play for the Brisbane Lions footy club, they gave me an opportunity in 2008."
Rocklff said he was excited about the prospect of the 2012 season.
"We're coming from the bottom and we're building to something special," he said.
Black's second place was the fourth time he has finished runner-up in his stellar career.
The 32-year-old Brownlow medallist averaged a career-high 26.8 disposals a match and was a model of consistency all season.
Lions vice-captain Jed Adcock (32.5) and Irish half-back revelation Pearce Hanley (32.5) rounded out the top five.
Although Black and Redden filled the minor places for the major award, they did not go home empty handed.
Black won the Players' Player award and Redden won the Shaun Hart Most Courageous Player award.
Patrick Karnezis was named the Rookie of the Year.
The full list of winners from the club champion awards was as follows:
Merrett-Murray Medal (Club Champion winner): Tom Rockliff
Nigel Lappin Trophy (Club Champion runner-up): Simon Black
Alastair Lynch Trophy (Club Champion third place): Jack Redden
Players' Player of the Year: Simon Black
Marcus Ashcroft Most Professional Player: Jed Adcock
Shaun Hart Most Courageous Player: Jack Redden
Rookie of the Year: Patrick Karnezis
Members' Player of the Year: Simon Black
Life Member Inductees: Jamie Charman and David Liddy
Merrett-Murray Medal voting
1. Tom Rockliff - 37.5 votes
2. Simon Black - 35.5 votes
3. Jack Redden - 35 votes
=4. Jed Adcock - 32.5 votes
=4. Pearce Hanley - 32.5 votes
6. Matthew Leuenberger - 31.5 votes
7. Ash McGrath - 25 votes
8. Todd Banfield - 22 votes
=9. Daniel Merrett - 20.5 votes
=9. Joel Patfull - 20.5 votes
Past winners
2010: Michael Rischitelli
2009: Jonathan Brown
2008: Jonathan Brown
2007: Jonathan Brown
2006: Simon Black
2005: Jason Akermanis
2004: Nigel Lappin
2003: Michael Voss
2002: Simon Black
2001: Simon Black, Michael Voss
2000: Michael Voss
1999: Justin Leppitsch, Jason Akermanis
1998: Chris Scott
1997: Matthew Clarke
