The Japan-EU statement is meant to confirm their stance of warning against such hardline policies of the Trump administration and mutually cooperating to firmly maintain the free trade regime.
European Affairs Minister Helen McEntee said trade between Ireland and Japan is worth more than €3bn a year, and will now expand further.
Japan's Minister for Economic Revitalisation, Toshimitsu Motegi, said on Tuesday: "At a time when protectionist measures are gaining steam globally, the signing of the Japan-EU deal today will show the world once again our unwavering political will to promote free trade".
Japan and the EU account for about a third of global GDP and their trade relationship has room to grow, according to EU officials, who expect the deal to boost the EU economy by 0.8% and Japan's by 0.3% over the long term.More news: UK PM defeats rebels over plans to remain in EU customs union
"We are sending a clear message that we stand together against protectionism".
The imported wine and cheese could hurt sales by Japanese wineries and dairies, but Japanese consumers have historically coveted such European products.
The deal, which is the largest-ever negotiated by the European Union, will unite about 600 million people across both markets.
Without mentioning Trump by name, Tusk made sharply clear that the agreement was intended as a counterpoint to Washington's current trade policy.More news: U.S. researchers discover 12 new moons around Jupiter
The US is proposing 10% tariffs on a 200 billion dollar (£151 billion) list of Chinese goods.
In a interview, the US President declared the European Union a "foe" of the United States.
Europe and Japan are rallying to bolster multilateral agreements as US President Donald Trump shuns such pacts and imposes tariffs on trading partners.
The major step toward liberalizing trade was discussed in talks since 2013 but is striking in the timing of the signing, as China and the USA are embroiled in trade conflicts.
Having started negotiations on the pact in 2013, the two sides reached an agreement in principle at the previous Japan-EU summit last July and then finalized their consultations in December. The partnership includes Australia, Mexico, Vietnam and other nations, although the USA has withdrawn. The EPA has raised Japan-EU relations to a new height, he said.More news: 8 players to watch at the 2018 Open Championship
Japan praised the deal with the European Union as coming from Mr Abe's "Abenomics" policies, created to wrest the economy out of stagnation despite a shrinking population and cautious spending. Japanese will get cheaper wine, pork and cheese, such as Parmesan, Gouda and cheddar, as well as chocolate and biscuits. Japan's growth remains heavily dependent on exports. But the Trump administration "closed the door" on the talks and subsequently slapped tariffs on EU steel and aluminum.New American tariffs on European cars could follow soon.