Ruiz Cirera, 28, is based in the British capital and was one of four photographers shortlisted for the annual award coordinated by the National Portrait Gallery.
The prize, handed out on Monday at the gallery, is worth 12,000 pounds ($19,200) to the winner.
More than 2,350 photographers submitted works for the prize, and a panel of judges whittled them down to 60 images which will go on display at an exhibition running from November 8-February 17, 2013.
Ruiz Cirera's winning picture captures a 26-year-old woman called Margarita Teichroeb, seated at a kitchen table and partially covering her face as she gazes at the camera.
It was part of a series called "Menonos", the photographer's long-term project to document the daily life of the pacifist and reclusive Christian-based Mennonite community living in Bolivia.
Ruiz Cirera travelled to South America several times, gradually winning the Mennonites' trust.
"I wanted Margarita to look at the camera, but that was a problem for her, and I guess that's why she is partially covering her face," he said.
"Her awkward expression says a lot about the tradition, isolation and lifestyle of this community ... They were willing to host me in their homes, but they weren't initially willing to be pictured. In some cases, it is forbidden.
"I stayed there for a month, living with different families, then returned a year later. That's when most of my pictures were taken."
The portrait was taken with a digital camera using only available light.
(Reporting by Mike Collett-White, editing by Paul Casciato)
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