In its second season of existence, Freo led by a goal at the final change before the Bombers pegged them back to claim the win.
The in-form Quenton Leach and Shaun McManus were major reasons behind Fremantle's good performance, while mobile ruckman Daniel Bandy was always dangerous.
Andrew Wills was also a crucial factor for the visitors, kicking five goals for the day.
Full forward Scott Cummings booted four for the Dons, while Mark Mercuri's inaccuracy was a problem, with 1.4 for the day.
James Hird, who would take home the Brownlow Medal at the end of the season in a tie with Brisbane’s Michael Voss, was once again impressive with 26 disposals and 10 marks.
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