"Songs of War: Music as a Weapon" made in 2010, beat films from Japan, Brazil and Britain to win in the category of arts programming.
The film follows composer Christopher Cerf, whose work includes more than 200 songs for the children's show "Sesame Street".
He said he was surprised and horrified when he realised that his music had been used to torture prisoners in Guantanamo Bay and Abu Ghraib.
"I was furious, on one level, and, I have to say, bemused on another," Cerf told Japan Today online news site in June. "It just seemed insane. And, of course, it hurt my feelings a little bit, too, that my songs were bad enough that anyone thought they'd be useful in this way."
Cerf and German filmmaker Tristan Chytroschek decided to find out how the music was used in torture and interrogation, and spoke with, among others, psychologists, prisoners tortured with Cerf's music, and a US soldier who had been a guard at Guantanamo Bay.
The International Emmys are awarded by the International Academy of Television Arts and Sciences, which has representatives from 50 different countries.
The last time a German show was honoured was in 2009, when the three-part docudrama "The Wolves" won, according to the Süddeutsche Zeitung newspaper. That film explored the issues surrounding the Berlin blockade, the division of Germany, and the country's reunification.