"In honoring them, we also send a message of hope to the millions of people they represent and for whom they work: human rights have no frontiers," PACE president Liliane Maury Pasquier said during a prize-giving ceremony.
The Vaclav Havel Human Rights Award — named after the famed former playwright, president of the Czech Republic and democracy activist — carries a prize of €60,000 ($65,500).
Enver Can of the Ilham Tohti Initiative, who represented Tohti at the event, vowed to continue efforts to free the Uighur economist, who was jailed for life in 2014 by a Chinese court on charges of inciting separatism.
The YIHR in the Balkans, founded in 2003, describes itself as a group campaigning for justice, equality, democracy and peace; it places particular importance on building cooperation between young activists from different countries and communities in the Balkans.
"Don't play deaf to the sound of war drums from the Balkans," warned Ivan Djuric, Serbian YIHR director, on accepting the prize. "We're not strangers; we're Europeans."
The 2019 shortlist also included Tajik human rights lawyer Buzurgmehr Yorov.
Last year's prize went to Russian activist Oyub Titiev. The 62-year-old heads the Memorial Human Rights Center in Grozny, the capital of Chechnya. Memorial is the last influential human rights organization still active in the troubled Russian republic in the North Caucasus.
The Council of Europe has been awarding the prize since 2013.
Vaclav Havel was at the forefront of the 1989 revolution that toppled four decades of communist rule before he became president.
Playwright Havel's underground theater riled authorities at the time of the 1968 Prague Spring, the first flowering of a democratic movement in what was then Czechoslovakia.
Havel went on to become a co-founder of the Charter 77 movement for democratic change. As the country's most renowned dissident, he suffered harassment from authorities and was subjected to repeated periods of imprisonment. He served as the last president of Czechoslovakia in 1992 and then as the first president of the Czech Republic from 1993 to 2003.