The Yokohama district court ruled in favour of some 7,000 people living near Atsugi Base, which is jointly operated by the US navy and Japan's Marine Self-Defence Force, saying Japanese planes must not fly between 10 pm and 6 am.
The ruling also ordered the Japanese government to pay about seven billion yen (USD 69 million) in compensation to plaintiffs, but said it could not tell the US military to ground its planes.
"The government does not possess power to order US forces in Japan to suspend flights," presiding judge Hiroyuki Samura said, public broadcaster NHK reported.
Japanese courts have previously turned down residents petitioning for a suspension of flights, but have ordered that the government pay compensation over noise.
Around 40,000 US military personnel are stationed in Japan under a security alliance. Most live in strategically located Okinawa, Japan's southernmost prefecture.
While many local economies are significantly boosted by the presence of bases, some people living nearby complain of the noise and danger of accidents, as well as the crimes committed by US service personnel.