The event was attended by dozens of government members, representatives of international organisations, civil society, the media and philanthropic foundations.
Javier Solana, the EU foreign policy chief, Mary Robinson, former Irish president, Paulo Coelho, the Brazilian writer and Wole Soyinka, the Nigerian author and Nobel laureate were expected to attend.
Zapatero presented the alliance idea to the UN general assembly in September 2004 as a way to overcome misunderstandings between the West and the Arab and Muslim world.
Turkey later become a co-sponsor of the project, which was adopted by the UN.
Before the opening opening ceremony, Recep Tayyip Erdogan, Turkey's prime minister, said: "In the Alliance of Civilisations process we have to achieve success. I am convinced that if we achieve success, we'll find an antidote against terrorism.
"One of the main reasons why the initiative has been supported is the extreme necessity and anxiety for tranquility and security which societies feel today."
The conference will include workshops on issues ranging from building cross-cultural understanding of conflict prevention, to religion and politics at the community level.
Zapatero said: "It aspires to build bridges that can help us to manage the differences existing in the world, particularly those linked to religious or cultural issues."
Organisers said they planned to announce details of a media fund aimed at supporting major film productions that promote cross-cultural understanding and combat stereotypes.
Attending the conference, Sheikha Mozah bint Nasser Al-Missned, chairwoman of the Qatar Foundation announced a $100m investment in a new initiative to tackle youth unemployment in the Middle East and north Africa.
The programme aims to connect young people to businesses and employment and is backed by a number of major corporations.