Knightsbridge restaurant Petrus knocked Ramsay's Chelsea flagship restaurant Gordon Ramsay into the number two spot, followed by Le Gavroche, The Ritz Restaurant and Pied a Terre, according to Harden's London Restaurants 2009 survey.
Petrus was part of Ramsay's restaurant empire, but Wareing takes full control of it next month after the owners of the Berkeley Hotel said that they wanted to work directly with him. It will be renamed Marcus Wareing at The Berkeley.
Ramsay and Wareing previously had a successful partnership, but fell out leading to a legal row over Petrus.
Ramsay suffered another blow with two of his restaurants, Gordon Ramsay and Claridges, in the most overpriced top 10 and the most disappointing cooking top 10.
However, there was some good news for the celebrity chef as his eponymous restaurant was named the top gastronomic experience ahead of Chez Bruce and Petrus.
The Wolseley topped the best for business list, followed by The Don, Bleeding Heart and The Square.
Meanwhile La Poule au Pot was named best for romance ahead of Andrew Edmunds, Bleeding Heart and Chez Bruce.
The Oxo Tower failed to impress, topping both the most overpriced and most disappointing cooking lists.
Best Overall (£80 a head plus)
1. Petrus
2. Gordon Ramsay
3. Le Gavroche
4. The Ritz Restaurant
5. Pied A Terre
Best for Business
1. The Wolseley
2. The Don
3. Bleeding Heart
4. The Square
5. 1 Lombard Street
Best for Romance
1. La Poule au Pot
2. Andrew Edmunds
3. Bleeding Heart
4. Chez Bruce
5. Clos Maggiore
Most Overpriced
1. Oxo Tower
2. Cipriani
3. Gordon Ramsay
4. Gordon Ramsay at Claridges
5. The River Cafe
Most Disappointing Cooking
1. Oxo Tower
2. The Ivy
3. Gordon Ramsay at Claridges
4. The Wolseley
5. Le Café Anglais
Top Gastronomic Experience
1. Gordon Ramsay
2. Chez Bruce
3. Petrus
4. Le Gavroche
5. La Trompette