The Trump administration has argued that Khalil, a Columbia University student, did not disclose past affiliations.
Prosecutors say they are prepared to go to trial for a third time after tension among jurors derails proceedings.
Japan said J-15 warplanes operating from two Chinese aircraft carriers in the Pacific carried out risky manouevres.
While the ruling does not order Khalil's immediate release, it does undermine the US government's case against Khalil.
Already qualified Japan beat Indonesia 6-0 in the final Group C game in the AFC qualifiers for the 2026 FIFA World Cup.
Jordanians are celebrating their football team's first qualification for a FIFA World Cup following win in Oman.
The failed mission comes two years after the Japanese start-up's first moonshot ended in a crash landing.
Tokyo and Beijing are closing in on a deal to allow Japanese seafood exports to resume following 2023 ban.