"The committee did not doubt for an instant that you deserved this award for your unshakeable faith that it was worth fighting for your points of view," editor Joern Mikkelsen said at the prizegiving ceremony in Copenhagen.
He said he was "proud" to give her the award, saying that "Hirsi Ali's fight for the freedom of expression is also our fight".
Hirsi Ali has been living under tight police protection since the murder of Dutch filmmaker Theo Van Gogh by an Islamic extremist in 2004.
She is threatened with death for her role in writing the script of Van Gogh's film "Submission", about the treatment of women under Islam. A note targeting her by name was found on his body.
Now living in the United States, she was in Copenhagen for the publication in Denmark of her new book "Nomad".
The Jyllands-Posten prize, worth 50,000 kroner (6,720 euros/8,880 dollars), was launched in 2006 at the height of anti-Danish protests in some Muslim countries after the paper published 12 cartoons of the Prophet Mohammed.
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