It was a big financial blow for the midlands club and also weakened caretaker boss Kevin MacDonald’s chances of being given the job on a permanent basis.
Gabriel Agbonlahor and Emile Heskey netted for Villa but Rapid refused to buckle and goals from Atdhe Nuhiu, Mario Sonnleitner and Rene Gartler stunned the near 30,000 crowd.
After 22 minutes Villa made their early supremacy count with Agbonlahor’s first goal of the season. The impressive Young was the provider with a teasing low ball across the box and Agbonlahor made no mistake from close range.
Agbonlahor tried to continue after suffering a knock to his leg and he was replaced after 40 minutes by Marc Albrighton.
And after 52 minutes Villa were stunned when Nuhiu brought Rapid back level on aggregate at 2-2.
Beye lost possession on the left flank and was then turned past by Veli Kavlak. His eventual cross was headed home at the near post in powerful fashion by Nuhiu who had also netted in the first leg a week ago.
Referee Eric Braamhaar pointed to the spot when Heskey was fouled by Sonnleitner after 72 minutes.
But Stiliyan Petrov’s spot-kick was saved to his right by Hedl before Heskey wasted the rebound.
Villa regained the lead after 76 minutes when Heskey chested home a volley from Habib Beye.
But the home side were stunned as Rapid struck twice in the space of three minutes.
First Guzan could only parry a header from Sonnleitner which still contained enough power to cross the line.Then in the 81st minute substitute Gartler converted a low centre from Christopher Trimmel.
ASTON VILLA: Guzan, Davies, Collins, Cuellar, Beye, Reo-Coker (Delfouneso 82), Petrov, Ireland, Ashley Young, Agbonlahor (Albrighton 40) Heskey.
RAPID VIENNA: Hedl, Dober, Sonnleitner, Soma, Katzer, Heikkinen, Pehlivan (Gartler 78), Kavlak, Hoffmann (Parocka 90+1), Saurer (Trimmel 73), Nuhiu.
Referee: Eric Braamhaar (Holland)