Japan Football Association vice president Kozo Tashima told a news conference: "We as the Japan Football Association reached the conclusion today that we will take part in the Copa America."
"We are preparing to send a letter to the South American Football Confederation about our participation."
The March 11 twin disasters severely damaged a nuclear power plant in the country's northeast, causing widespread electricity cuts that forced the temporary suspension of the J-League.
The league has rescheduled its backlogged fixtures to be played during a break in July, which clashes with the South American championship, where Asian champions Japan are invited as non-member guests along with Mexico.
J-League clubs have said they are opposed to sending top players to the July 1-24 Copa America in Argentina.
But the Japan Football Association decided at an executive meeting Thursday that it would send a squad mostly made up of Europe-based players who will be having a pre-season break in July, an association official said.
JFA president Junji Ogura said earlier he had been given assurances that world football's governing body FIFA was considering an exceptional measure to require European clubs to free up Japanese players for the Copa, despite their guest status.