The restaurant in Girona (Gerona), run by three brothers and known for its dishes based on perfumes, had spent two years as runner-up on the World's 50 Best Restaurants list compiled for a 12th year by more than 900 international experts for Britain's Restaurant magazine.
It swapped places with Noma, the two Michelin-starred Danish restaurant which spent three years at the top but which apologized in March after it left 63 customers suffering from vomiting and diarrhoea over a five-day period.
The magazine said that El Celler de Can Roca "gained global acclaim for its combination of Catalan dishes and cutting edge techniques and the passion that they share for hospitality".
Joan Roca heads the kitchen while his brother Jordi is pastry chef and Josep is head sommelier and in charge of front of house. They make what the magazine called a "formidable team" that creates "emotional cuisine" which takes diners back to childhood memories, the magazine said.
Spain continues to dominate the top 10 with Mugaritz in San Sebastian at number four, and Arzak, also in San Sebastian, at number eight.
Italy's Osteria Francescana was in third place, up from fifth, while New York's Eleven Madison Park was up five places to fifth, in the awards presented on Monday night at London's Guildhall.
South America also had much to celebrate in the results with a record six restaurants from the continent on the list. They are led by Brazil's D.O.M., run by former DJ Alex Atala in Sao Paulo, at number six and Astrid Y Gaston in Lima, Peru, the highest climber in the list, rising 21 places to 14.
Asia meanwhile boasts seven restaurants in the top 50, up one from last year, led by Tokyo restaurant Narisawa at number 20. Australia's Attica is meanwhile the highest new entry on the list at 21.
The United States has six restaurants on the list, as does France, with legendary chef Alain Ducasse winning a lifetime achievement award.
British chef Heston Blumenthal kept two restaurants in the top 50 with his London restaurant Dinner up two places at seven, although his older restaurant The Fat Duck fell 20 places to 33.
The One to Watch award went to the Test Kitchen in South Africa's Cape Town, where British-born chef Luke Dale-Roberts has an "eclectic style" that produces "unequivocally delicious food," the magazine said.
The result caps a rough few months for Noma, which had seized the top spot in 2010 from the now-closed El Bulli in Spain and held it in 2011 and 2012 with its innovative mix of foraged ingredients in a quayside setting.
Inspectors from the Danish food ministry criticized the restaurant in March for not alerting authorities quickly enough and for failing to take adequate action after a kitchen worker fell sick, meaning that the illness spread to customers.
Noma blamed internal communication problems for failing to disinfect the kitchen quickly enough.
Top 10 of Restaurant magazine's 50 Best Restaurants 2013 (last year's rank in brackets):
1. El Celler de Can Roca — Girona, Spain (2nd)
2. Noma — Copenhagen, Denmark (1st)
3. Osteria Francescana — Modena, Italy (5th)
4. Mugaritz — San Sebastian, Spain (3rd)
5. Eleven Madison Park — New York, USA (10th)
6. D.O.M. — Sao Paulo, Brazil (4th)
7. Dinner by Heston Blumenthal — London (9th)
8. Arzak — San Sebastian, Spain (8th)
9. Steirereck — Vienna, Austria (11th)
10. Vendome — Bergisch Gladbach, Germany (23rd)