Chinese Commerce Minister Gao Hucheng and Swiss Economy Minister Johann Schneider-Ammann inked the accord in a ceremony at the Commerce Ministry in Beijing before officials and reporters.
Afterwards, they clinked glasses of champagne in celebration of the agreement, which aims to increase the USD 26.3 billion in bilateral trade they recorded in 2012.
China in April signed its first FTA with a European country -- non-EU member Iceland -- but Saturday's deal marks the first with an economy in mainland Europe.
"This free trade agreement has an important significance for the relationship between the two countries," Schneider-Ammann told AFP after today's signing ceremony.
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He noted that China is the world's single biggest developing market with potential for a growing middle-class.
Fiercely independent Switzerland is not a member of the EU and even waited decades to join the United Nations.
Nonetheless, it is an economic heavyweight known for high-value luxury goods such as its world famous watches and as a financial centre.
Switzerland mainly sells watches, pharmaceuticals and chemicals, as well as machinery to China, which ships mostly textiles and machinery back to Switzerland.
Switzerland and China had signed a preliminary FTA agreement in May during a visit to the landlocked European nation by Chinese Premier Li Keqiang.
Schneider-Ammann said the deal is also important for hedging risks.
"We get a chance to spread out the risk of the Swiss economy a little bit over the borders of our European neighbourhood," he said. "It has a great importance."
The EU economy has experienced serious turmoil over the past several years in the wake of the global financial crisis and due to sovereign debt instability that engulfed Greece and other member states including Spain, Italy and Portugal.