Published in The Waitrose Good Food Guide, Chef Simon Rogan's restaurant in Cartmel, Cumbria, took the top spot for the first time, pushing Heston out the way.
Using independent inspectors to secretly review restaurants, the guide has been running since 1951.
Both restaurants scored a perfect 10 in the rankings, L'Enclume for the second year in a row, The Fat Duck for the sixth year in a row.
'Rogan rightfully takes his place as leader of the pack when it comes to modern British cooking,' said the guide's consultant editor Elizabeth Carter.
'His fantastic way with seasonal ingredients from the Cumbrian land and coast brings dishes that are a joyful celebration of this county's magnificent diversity. L'Enclume is truly deserving of the number one spot,' she continued.
Clearly chuffed, chef Rogan said, 'I'm so proud of my staff and this phenomenal achievement with the Good Food Guide. This is something we have always dreamed about. We have received this accolade because of our focus on both the food product and the customer - keeping it natural and fresh in the kitchen, and friendly but professional in the dining room.'
The 2014 edition sees no new names enter the top 10, with Nathan Outlaw's seafood restaurant in Cornwall taking third place, Sat Bains in Nottingham and Restaurant Gordon Ramsay in London taking fourth and fifth.
Jason Atherton's Pollen Street Social, London, remained in sixth place, followed by Hibiscus, The Square and The Ledbury, all also in the capital. Raymond Blanc's Le Manoir aux Quat'Saisons in Oxford rounded up the top 10.
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