Fugitive US intelligence analyst Edward Snowden, who leaked details of secret surveillance programmes, and a group of jailed Belarus dissidents, had been in the running for the prestigious £42,000 Sakharov award.
Previous winners include Nelson Mandela and Burmese activist Aung San Suu Kyi.
Europe's three major political groups had nominated Malala in a show of united support for her cause.
"The European Parliament acknowledges the incredible strength of this young woman," said Martin Schulz, president of the EU legislature.
"Malala bravely stands for the right of all children to be granted a fair education. This right for girls is far too commonly neglected."
The chairman of the conservative European People's Party (EPP), Joseph Daul, added: "Today, we decided to let the world know that our hope for a better future stands in young people like Malala Yousafzai."
But the Pakistani Taliban claimed the teenage activist had done "nothing" to deserve the award, and vowed to try to kill her again.
A spokesman said: "She has done nothing. The enemies of Islam are awarding her because she has left Islam and has become secular."
Malala was shot in the head by the militant group in October last year for campaigning for girls' schooling.
The attack sparked international condemnation, and following treatment in Britain, she has gone on to become a global ambassador for the right of all children to an education.
Malala now lives in the UK with her family, but has spoken of her plans to return to Pakistan when she has received a full education and is "fully empowered".
The Sakharov prize for freedom of thought has been given by the European Parliament each year since 1988 to commemorate Soviet scientist and dissident Andrei Sakharov.
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