The accord is expected to benefit Japanese auto makers Toyota, Nissan, Suzuki and Mazda by removing 10 percent tariffs on Japanese cars.
Japanese auto parts makers Denso, Aisin Seiki, and JTEKT also stand to gain from the fall of a 3 per cent tariff on auto parts.
Europe's food sector is the other big winner, especially in high-quality regional specialities. Japan imposes high tariffs on imports of premium European food and drink products, including wines, cheese, chocolate, meats and pasta.
Japanese trading house Kanematsu Corp, beverage maker Kirin Holdings and drinks maker Asahi import wines from Europe and could see higher profits once wine tariffs fall.
French suppliers Pernod Ricard and Louis Vuitton Moet Hennessy should also benefit from a reduction in tariffs for premium liquors, wines and spirits.
EU exports of processed food, including meat and dairy products, are expected to rise by up to €10 billion once the deal takes full effect and tariffs are gradually dropped, the European Commission says.
Japanese dairy companies such as Meiji and Megmilk Snow Brand will face greater competition. They are protected by tariffs of up to 40 per cent on processed cheese, which will slowly be removed. Megmilk has two-thirds of the domestic market for soft cheese and could lose customers.
Competition in the dairy sector will come from European firms such as Danone, Lactalis and Nestle.
Meat products were the largest single EU food export to Japan in 2017. Exporters from Denmark and Spain hope to capitalise on growing Japanese demand for speciality processed meats such as ham, salami and cured bacon.