The Primera Liga side claimed their place in the last 16 of the competition with the victory on Wednesday, in a game played behind closed doors following a UEFA imposed punishment for crowd problems at Atletico's 2-1 home win over Olympique Marseille in October.
PSV and Atletico were greeted with an empty silence as they took to the pitch in a bitterly cold, windswept 55,000 seat stadium to complete the pre-match formalities.
At one end of the Calderon a banner was draped over the seats from the home supporters saying: "Absolutely no one will separate us from you," and they did not disappoint.
Just before kick-off a few hundred Atletico fans gathered outside one of the open corners of the Calderon, and started to cheer the side on, and continued to do so throughout.
"I want to thank the fans for everything they have done because inside we could hear them singing," Argentina striker Sergio Aguero said.
"That said, the experience of playing without fans was an ugly one because we would have preferred them inside with us."
French striker Florent Sinama Pongolle added: "I heard the fans singing and shouting outside. It was very important and it's something we'll always remember."
When Atletico's Simao Sabrosa and Maxi Rodriguez scored in the first half the fans could be heard cheering outside after a short delay, while inside the club played a recording of fans celebrating.
Danny Koervermans' goal for PSV at the start of the second half was met with total silence.
