The 31-year-old star also beat his "Avengers Assemble" co-star Robert Downey Jr to the title of Total Film magazine's Hottest Actor, with the superhero blockbuster also scooping the Hottest Film gong.
"I am absolutely astonished. To anyone and everyone who voted for me: thank you. To be nominated in such exalted company was honour enough, but this really is the icing on the cake," Hiddleston said.
"Actors can't call themselves actors without an audience to watch them, and the idea that you're all out there and believing in the work I do is a source of enormous pride," he added.
More than 240,000 readers voted for the British star, who also beat off stiff competition from the likes of Christian Bale.
"Avengers Assemble" proved hugely popular with film fans, who awarded the superhero film the Hottest Scene award and Hottest Director for Joss Whedon, as well as the coveted Hottest Film title. Peter Jackson's "The Hobbit: An Unexpected Journey" has been branded the most anticipated film event of the year, winning Hottest Trailer.