"This is the biggest trade agreement we have ever negotiated for the European Union," EU trade chief Cecilia Malmstrom said.
"It sends a powerful message in defence of open trade based on global rules."
In the past five months, negotiators worked on stabilising tariffs in services, regulatory cooperation and the means to protect food and drink categories so that, for example, only sparkling wines from a specific Italian region can be called prosecco.
Discussions will continue on the contentious issue of investor protection. Japan has been reluctant to adopt the investment court system the EU has devised as an answer to fierce criticism that disputes between foreign companies and states should not be settled by opaque tribunals.