Hawthorn led 5.5 (35) to 1.6 (12) after a fast-paced but low-scoring first half - the first since 1960 to see only six goals scored.
Playing in their first-ever Grand Final, Fremantle narrowed Hawthorn's lead to 6.5 (41) to 5.8 (38) midway through the third quarter, but late goals by Luke Breust and Bradley Hill allowed the Hawks to hold on and to claim their first AFL title since 2008.
Hawthorn were top qualifiers after the regular season and were playing in the Grand Final for the third time in six years. Their end-to-end win — Gunston kicked the opening goal after 3 minutes, 39 seconds — allowed them to finally shed a reputation as under-achievers after their upset, 10-point loss to Sydney in last year's grand final and their three-point loss to Collingwood in the 2011 preliminary final.
They remain the only club to have won at least one premiership per decade since the 1960s, accumulating 11 titles since 1961.
A total of 10 Hawthorn players became two-time premiership winners, including Shaun Burgoyne, who won with Port Adelaide in 2004 and superstar Lance Franklin, who kicked one goal in the first quarter in another quiet match.
Coach Ross Lyon, who led Fremantle into the premiership decider for the first time in their 19-year history, remained without a win in four Grand Finals. He guided St. Kilda to the premiership deciders in 2009 and 2010, when a replay was needed to find the champion.
Hawthorn coach Alastair Clarkson won the premiership for the second time in his nine-year reign.
Gunston's three first-half goals were crucial in a close-fought match, in which Fremantle didn't kick their first goal — through Tendai Mzungu — until the 12th minute of the second quarter.
By that stage Hawthorn had four goals and Gunston strengthened their position when he followed Mzungu's major with his third goal.
In a match which was occasionally made scrappy by wet conditions, Fremantle dominated the ruck in the first half through Aaron Sandilands without turning possession into points. Midfielders David Mundy, Nathan Fyfe, Michael Barlow and Stephen Hill led Fremantle's strong start to the third quarter when it kicked five of the first seven goals.
But Fremantle paid for their inaccuracy, putting four shots out on the full and wasting late chances by kicking 2.4 in the final quarter.
Brian Lake won the Norm Smith Medal as the best afield, claiming his first premiership medal after losing three preliminary finals with the Western Bulldogs.
Jordan Lewis, Josh Gibson, Grant Brichall and Cyril Rioli, who laid seven tackles, were also prominent for Hawthorn while Fremantle tagger Ryan Crowley kept Sam Mitchell to just 12 touches.