The deal signed on the sidelines of a meeting of EU transport ministers in Luxembourg will see the market gradually opened up over the next five years until all restrictions are lifted by 2018.
All airlines from the 27-nation bloc will be able to fly direct to Israel and Israeli carriers will be allowed to fly to airports throughout the EU, the European Commission said in a statement.
EU Transport Commissioner Siim Kallas said the deal showed that Israel was a "key partner for the EU.
In April, Israeli airline employees went on strike for two days against the agreement, saying that it would lead to job losses.
The EU is the biggest aviation market for Israel, accounting for 57 percent of scheduled international air passenger movements to and from the country. In 2011, EU-Israel traffic amounted to 7.2 million passengers.