The agreement deals "another blow against tax evaders, and (represents) another leap towards fairer taxation in Europe," said Pierre Moscovici, the EU commissioner for tax issues.
Moscovici signed the accord, which takes effect in 2018, along with Jacques de Watteville, the Swiss secretary of state for international financial matters, and Latvian Finance Minister Janis Reirs, whose country currently holds the EU presidency.
"The EU led the way on the automatic exchange of information, in the hope that our international partners would follow," Moscovici said in a statement.
"This agreement is proof of what EU ambition and determination can achieve."
Under the accord, the EU and Switzerland will automatically exchange information on the bank accounts held by their respective residents beginning in 2018.
However, the Swiss federal government emphasized that this exchange of information would only take place "once the necessary legal basis has been created".
The government also said the agreement is subject to consultation and ratification in Switzerland.
Interested parties and the country's 26 cantons have until September 17th to comment on the deal with the EU.
After that the federal government will submit a text for the two houses of parliament to consider.
Despite these caveats, the European Commission praised the agreement as a step forward in the fight against tax evasion.
"This new transparency should not only improve member states' ability to track down and tackle tax evaders, but it should also act as a deterrent against hiding income and assets abroad to evade taxes," the European Commission said.
The EU executive is negotiating similar accords with Andorra, Liechtenstein, Monaco and San Marino that are expected to be signed by the end of the year.