They are the 12th winners of the prize, which is awarded every three years and is named after its inaugural winner – prolific Finnish architect Alvar Aalto, who designed the medal. Fuensanta Nieto is also the first woman to be recognised by the award in its 48-year history.
The jury, which included Dutch architect Wessel de Jonge and Danish architect Dorte Mandrup-Poulsen, said the studio's work restored their faith in the adaptability of contemporary western architecture.
"The work of Nieto and Sobejano demonstrates how an architect's cultural background can inspire architecture of outstanding quality and expressive power. Nieto and Sobejano's work has a primal energy ranking it among the world's most compelling statements and groundbreaking achievements in architecture," they commented.
The architects earned international recognition following the 2008 completion of their Madinat al Zahra Museum in Córdoba, Spain. They followed that up with an extension to a museum inside a ruined castle in Germany, and the perforated-aluminium-clad San Telmo Museum extension in San Sebastián.
More recently, they won the competition to design a woodland cultural centre for the organisation run by Estonian composer Arvo Pärt, seeing off competition from Zaha Hadid, Coop Himmelblau and Henning Larsen Architects.
"Their portfolio is varied and instantly recognisable, maintaining outstanding standards of creative excellence, informed by a philosophy of respect for human life and the environment," said Finnish architect Rainer Mahlamäki, the jury chairman.
"Nieto and Sobejano proudly carry on a tradition of humanism in architecture."
The medal is jointly awarded by the Museum of Finnish Architecture, the Finnish Association of Architects SAFA, the Architectural Society, the Alvar Aalto Foundation and the City of Helsinki. Past winners include James Stirling, Jørn Utzon, Tadao Ando and Alvaro Siza.
The announcement was made yesterday at a seminar marking Architecture Day in Helsinki. An exhibition for the prize runs at the Museum of Finnish Architecture until 1 March.
Photography is by Roland Halbe, apart from where otherwise indicated.