The Japanese duo sensationally came from behind to defeat Denmark's Christinna Pedersen and Kamilla Rytter Juhl 18-21, 21-9, 21-19 in a thrilling encounter.
The match was locked at 16-16 in the final game as the Danes and Japanese traded point for point. Denmark raced ahead to 19-16 and looked like they were heading for victory, only to be stunned by their counterparts.
Japan won four points on the bounce to go 20-16 ahead, eventually edging the game by just two points.
"We gave it everything we had. I just wish we could turn back time to when it was 19-16, because that's when it went too quick for us," a disappointed Pedersen told TV2 Sport.
Danish silver medallists Christinna Pedersen and Kamilla Rytter Juhl stand together on the podium. Photo: REUTERS/Ruben Sprich/Scanpix
Earlier in the day South Koreans Jung Kyung-Eun and Shin Seung-Chan had defeated China's Tang Yuanting and Yu Yang to claim bronze.
Pedersen and Juhl's silver was Denmark's eleventh medal at the Rio Games.