The software engineer, who worked on the operating system kernel for more than two decades, will share the gong with stem cell scientist Dr Shinya Yamanaka.
Technology Academy Finland honoured Torvalds for his influence in the fields of "shared software development, networking and the openness of the web".
"This recognition is particularly important to me, given that it's given by the Technology Academy of Finland," Tovalds said.
"I'd also like to thank all the people I've worked with, who have helped make the project not only such a technical success, but have made it so fun and interesting."
The Linux kernel is one of the most prominent examples of free and open source software. It was first released in 1991, when Torvalds was a student at the University of Helsinki.
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This was the first time that the biennial Millennium Tech Prize has been shared. Each winner was awarded €600,000 (£483,000).