Boyd polled 154 votes to oust last year's winner in Cross, whose round 20 ankle injury saw his own tally stall. He finished runner up with 145 votes, while defender Dale Morris (133) came in third.
The accolade, which comes as a first for Boyd, caps off a sterling year for the 27-year-old. He ended the season with an average of nearly 29 disposals across his 25 games, and recorded 30 or more possessions on nine separate occasions.
The 140-game player was also named in his first All-Australian side last month.
It looked like Cross, 26, was headed for back-to-back honours after he led the count for most of the night.
But, the ankle problem that required surgery and saw him miss rounds 20 and 21, combined with Boyd's solid games against Geelong and Collingwood, saw the latter take home the grand prize.
Captain Brad Johnson, who became the Bulldogs' games record holder this season, demonstrated his champion ability to come in fourth with 131 votes in what was his 16th season.
And, Boyd's All-Australian teammate Brian Lake, who claimed the club's top medal two years ago, came in fifth with 125 votes.
Other award winners included Jarrod Harbrow (Community Award), Wayde Skipper (Williamstown's most outstanding Western Bulldogs player), Liam Picken (best first year player), Callan Ward (most promising player), and Ryan Hargrave (Match Committee Award), while Morris also claimed the Scott West Most Courageous Player Award.
2009 Charles Sutton Medal Results
1. Matthew Boyd 154 votes
2. Daniel Cross 145 votes
3. Dale Morris 133 votes
4. Brad Johnson 131 votes
5. Brian Lake 125 votes
6. Jarrod Harbrow 123 votes
7. Adam Cooney 110 votes
8. Shaun Higgins 96 votes
9. Ryan Hargrave 93 votes
10. Jason Akermanis 86 votes
