"In the analysis we did, we were speaking a lot about the usual position of Neuer, which is high," Emery said of Villa's pre-match conversations.
"He (Duran) had in his mind this possibility about Neuer."
The 20-year-old Colombian electrified Villa Park with his 79th minute goal, receiving a long ball then hooking it over Neuer who had come off his line as he did often in the game.
"He is young, he has huge potential," added his delighted boss. "As a player, I have to let him play, put him on the field, because his talent is there, his capacity to help us."
It was Duran's fifth goal as a substitute this season.
"We are working with him. Most important is his attitude. He's available to play 90, 60, 30 minutes. He's been focusing each minute he's playing," he said.
"It's fantastic for him and the team."
Emery also had warm words for goalkeeper Emiliano Martinez, who kept Bayern at bay with a string of great saves, none better than a last-gasp dive to defy a Harry Kane header.
"Martinez did an amazing job, amazing saves," Emery said.
The win left Villa with two wins out of two in the new Champions League format consisting of a 36-team league in the first phase.
"I can feel proud of our work, how we are getting better," Emery said, praising the Villa fans for creating a thunderous atmosphere against a team they famously beat in 1982 to lift the European Cup.
