The SUV beat the likes of the Toyota 86 and Subaru BRZ sports car twins to become the first Mazda to win its domestic Car of the Year since the MX-5 in 2005.
The CX-5, the first Mazda to be designed from the ground up with the company's full range of efficiency-focused Skyactiv technologies, is also the first non-electric car or non-hybrid to win the gong since 2008.
Winners for the past three years have been the Nissan Leaf (2011), Honda CRZ (2010) and Toyota Prius (2009).
Japan's Car of the Year committee comprises 60 of the country's automotive experts and journalists.
Contenders must have gone on sale locally between 1st November 2011 and 31st October 2012, and be sold in more than 500 units, to be eligible.
The BMW 3 Series won the Import of the Year award.