The company, entering the competition for the first time, scooped the supreme award for its No Catch...Just Cod product, which was also named best product in the fish and seafood category of the retail awards, and the savoury section of the foodservice category.
Judges said they had been impressed by the product's innovative packaging, great taste and ethical credentials.
A spokesman for Johnson Seafarms said: "Our fish meets the consumer's insatiable love of cod but in a way that avoids further depletion of the world's rapidly diminishing fish stocks."
No Catch...Just Cod is to roll out to 160 Tesco stores at the end of the month.
Other winners on the night included Galloway Lodge Preserves for its relish marmalade, Rannoch Smokery for its range of smoked meats, The Craigmyle Cheese Company for its Wummle cheese, and Island Bakery Organics for its sweet biscuits.
Mackays claimed the award for international business of the year for its marmalades, preserves, chutneys and relishes made from Scottish-sourced fruit and vegetables, while Benromach's Classic
55-year-old malt whisky won the award for brand development. The prize for the most successful product from last year's awards went to RR Spink & Sons for its range of ready-to-eat delicatessen fish.
Winners at the event, organised by the Royal Highland and Agricultural Society, were selected from more than 50 shortlisted products in six categories: retail, foodservice, international business, brand development, direct marketing and healthy eating.
Other sponsors included Scottish Development International and the Scottish Executive's Healthy Living Campaign.