Tutu was on Monday awarded the prize for "his exceptional contribution to building a universal culture of human rights at the national, regional and international levels".
The jury highlighted the role he played in building the new non-racial South Africa and his contribution as head of the Truth and Reconciliation Commission to national reconstruction which became a model for other post-conflict societies, the United Nations Educational, Scientific and Cultural Organisation (Unesco) said in a statement.
Tutu's daughter was in the UN cultural organisation's Paris headquarters to receive the award on behalf of her father.
The biennial Unesco/Bilbao prize was established in 2008 after an endowment from the city of Bilbao in Spain. It includes a $30 000 cheque, a diploma and a bronze trophy.
Tutu and two other Nobel Peace laureates last month wrote to the Nobel foundation in protest at the decision to award the 2012 prize to the European Union.
The "EU is clearly not 'the champion of peace' that Alfred Nobel had in mind when he wrote his will," they said in an open letter.
The letter was also signed by Northern Ireland's Mairead Maguire, who won the prize in 1976, and Argentina's Adolfo Pérez Esquivel in 1980. – Sapa-AFP