The eatery received hundreds of votes in the nomination stage of the competition, which attracted 400 entrants and 24,000 votes nationwide.
From 15 regional finalists, the public's high praise for Paper Moon was endorsed by a team of judges including hospitality industry guru Kerry Tyack and New Zealand's first Master of Culinary Arts, Mark Gregory.
Chief judge Mr Tyack said Paper Moon had a lively atmosphere, exceptional service and "a comprehensively mouth-watering menu".
The winning meal was "generous, innovative and downright Kiwi".
The dish will feature on the popular television segment Food in a Minute.
The episodes are being filmed at the cafe this week and screen on TV One and TV2 from November 26.
The win ensures the recipe will be emailed to the Food in a Minute database of more than 100,000 fans, feature on recipe cards in-store at supermarkets, and appear on the Food in a Minute and Cafe of the Year websites and Facebook pages.
Mrs Kaynarcali said they entered the competition after a customer told staff they "must" put forward the beans and bacon dish.
Mr Kaynarcali, the chef, and Mrs Kaynarcali, front of house, said they took inspiration for their diverse New Zealand cuisine "with a twist" from their world travel.
"We are from Istanbul but we have been living in New Zealand for 16 years and love the people and the culture here. Our food is not influenced by Turkish cuisine - more the Kiwi chefs we work with and inspiration from our travels."
Signature dish
Paper Moon, Mairangi Bay
Baked beans with pan-fried chorizo and onion, delicately blended with a smoked tomato relish, served on a toasted bagel, layered between slices of bacon, topped off with a poached egg and drizzled with buttery hollandaise sauce.