Prince William, along with over 40,000 Villa fans, helped to inspire Emery's team to overcome the significant disparity in Champions League experience between the two sides.
Britain's future King was among those to congratulate Emery in a meeting after the match.
"I told him the best moment we can pass is days like today," said Emery.
"I don't know where (Villa can go) but we are going to try to enjoy the way. Today we (will) remember how we played, who we played and the Champions League final from 42 years ago. It was a special day."
Just five years ago Villa were languishing in the second tier of English football, but they have enjoyed a meteoric rise since the Spaniard took charge under two years ago.
After a comfortable 3-0 win over Young Boys in Switzerland two weeks ago, the visit of the six-time European champions was the sort of glamour tie Villa fans had been relishing and it did not disappoint.
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Harry Kane overcame an ankle injury that forced him off late on in Bayern's 1-1 draw against Bundesliga champions Bayer Leverkusen at the weekend to start.
Bayern had averaged over four goals a game in their opening seven matches under Kompany, including a 9-2 thrashing of Dinamo Zagreb to open their Champions League campaign.
They dominated the ball early on, but Kane's header from an offside position that was well saved by Emi Martinez was the closest they came to breaking through Emery's well-organised defence.
"They're a strong team, and this place is not an easy place," said Kompany. "I don't think the performance was perfect, but it wasn't a bad performance."
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Villa did have the ball in the net midway through the first half when Torres prodded in at the back post from a free-kick.
However, Jacob Ramsey had strayed offside in the build up and Villa's jubilant celebrations were cut short.
Michael Olise was another of Bayern's stars making a return to England and the former Crystal Palace winger was only denied the opener before half-time by a stunning save from Martinez.
Kompany had surprisingly left Jamal Musiala on the bench but the German international was summoned to make an impact at half-time.
Musiala nearly weaved a way through the Villa defence on the hour mark but his shot was blocked by Torres.
Instead, it was Villa's own super sub that came on to win the game.
Five of Duran's six goals this season have come as a substitute.
The 20-year-old showed his strength to hold off Dayot Upamecano and lift the ball over the stranded Neuer.
Villa still needed their own goalkeeper to make important interventions at the other end to seal a historic victory.
Musiala's pass finally unlocked the home side's defence but Serge Gnabry could not beat Martinez.
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The Argentine then produced an even better save deep into stoppage time to turn Kane's header to safety.
(This story has not been edited by staff and is auto-generated from a syndicated feed.)