Spanish restaurants "Disfrutar" in Barcelona and "Diverxo" in Madrid came third and fourth.
Inspired by nature, Kofoed's restaurant received the first three Michelin stars for Denmark in 2016.
The awards named Colombian Leonor Espinosa as the "world's best female chef" and her restaurant Leo was ranked 48th in the list.
Despite France's famed cuisine, only three French restaurants—all in Paris—featured in the top 50: "Septime" in 22nd, "Le Clarence" in 28th and "Arpege" in 31st.
The list is selected by 1,080 independent culinary experts including chefs, specialist journalists and restaurant owners who note their experiences in the past 18 months under the aegis of the magazine.
The experts are divided up into 27 regions with 40 voters each and they can each vote for 10 restaurants including at least three outside their region.