Borrell and his Japanese counterpart Takeshi Iwaya unveiled the pact to develop cooperation on joint military drills, the exchange of information related to the defence industry, and space security among other matters.
"I am extremely pleased to be here with Minister Iwaya to announce the conclusion of this security and defence partnership between the European Union and Japan," Borrell said.
He called it the "the first agreement of this nature" the EU has made with an Asia-Pacific country, describing it as "historical and very timely".
"We live in a very dangerous world" and "given the situation in both of our regions, this political framework deepens our ability to tackle emerging threats together", Borrell told reporters.
He did not mention China, but Japan has previously called its neighbour its greatest security challenge as Beijing builds up military capacity in the region.
After the Tokyo talks, Borrell heads to South Korea, where concerns about North Korea will top the agenda.
The United States has said thousands of North Korean troops are in Russia readying to fight in Ukraine.
Pyongyang also test-fired one of its newest and most powerful missiles on Thursday, demonstrating its threat to the US mainland days ahead of elections.
- Defence industries -
The text of the EU-Japan Security and Defence Partnership, seen by AFP, said they would promote "concrete naval cooperation" including through activities such as joint exercises and port calls, which could also include "mutually designated third countries".
It also said the EU and Japan would discuss "the development of respective defence initiatives including exchange of information on defence industry-related matters".
Japan, which for decades has relied on the United States for military hardware, is also developing a new fighter jet with EU member Italy and Britain set to be airborne by 2035.
The agreement on industrial cooperation could "turbo-charge collaboration, such that joint defence projects between Japanese and European firms funded through EU mechanisms may be on the cards", analyst Yee Kuang Heng of the University of Tokyo's Graduate School of Public Policy told AFP.
Japan is ramping up defence spending to the NATO standard of two percent of GDP by 2027, partly to counter China, which is increasing military pressure on Taiwan.
Beijing claims the self-ruled island as part of its territory and has not ruled out using force to bring it under its control.
Japanese Prime Minister Shigeru Ishiba, who could head a minority government after a disastrous general election last week, has said that "today's Ukraine could be tomorrow's East Asia".
Ishiba has also called for the creation of a NATO-like regional alliance with its tenet of collective security, although he has conceded this will "not happen overnight".
The same warning was issued by Ishiba's predecessor Fumio Kishida, who was hosted by US President Joe Biden for a state visit in April at which the allies announced plans to boost their defence partnership.
On Friday, Borrell and Iwaya also "exchanged an instrument of ratification for Japan EU Strategic Partnership Agreement, or SPA", Iwaya said, referring to a separate, previously agreed pact.
"This SPA will formally enter into force on January 1 next year. It will be a legal foundation to strengthen the Japan-EU strategic partnership into the future," Iwaya said.
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