The Victoria's Secret model topped the annual poll, preventing Cheryl Cole from securing her third consecutive win.
Huntington-Whiteley will appear in Transformers: Dark of the Moon, replacing Megan Fox who falls two places to number four.
"Wow! Thanks for voting guys, I'm so flattered to be FHM's Sexiest Woman in the World," she said of her win. "This is a really exciting year for me and I hope you all enjoy Transformers 3."
X Factor judge Cole fell outside the top 10 to number 12, while both Katy Perry and Rihanna enjoyed high jumps to number two and three respectively.
Commenting on the results, FHM's Stuart Hood said: "Queen Cheryl is dead and succeeding her on the throne is a British sensation who is no stranger to stepping into the high heels of the world's most attractive women.
"In the last 12 months, actress and model Rosie Huntington-Whiteley has replaced Kelly Brook in Jason Statham's heart and replaced Megan Fox in Transformers, and now she's replaced Wor Chezza as the planet's most lusted after female."
Kate Middleton, the new Duchess of Cambridge, is the only royal to make the top 100, debuting at number 39. Doctor Who actress Karen Gillan is a new entry at 42.
The top 10 in full is:
1. Rosie Huntington-Whiteley
2. Katy Perry
3. Rihanna
4. Megan Fox
5. Olivia Wilde
6. Brooklyn Decker
7. Marisa Miller
8. Kelly Brook
9. Nicole Scherzinger
10. Irina Shayk
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