Gabriel Agbonlahor benefited from some calamitous Hull defending to put the visitors ahead in the 13th minute but only Kevin Kilbane will know how he failed to draw the Tigers level midway through the first half.
The crucial second goal arrived 15 minutes from time, James Milner picking himself up to convert from the penalty spot after he had been fouled by George Boateng.
Hull were, however, grateful for news Jan Vennegoor of Hesselink had regained consciousness after being knocked out in a challenge with Richard Dunne at the start of the second half.
The Tigers presented their opponents with the opening goal in the 13th minute.
First Ibrahima Sonko and then Paul McShane saw their attempted clearances charged down and Agbonlahor curled a pinpoint shot into the top corner from a tight angle.
Having been under the cosh, Hull squandered an unbelievable opening in the 24th minute. Kilbane played in Vennegoor of Hesselink but Brad Friedel blocked his effort from eight yards.
The ball fell to Kilbane, who first had a shot saved by Friedel, then, having retrieved the ball with only James Collins to beat on the line, saw his second attempt deflected over the bar via the defender’s arm.
Hull had another glorious opening within two minutes of the restart. A long throw from Sonko found its way to defender Steven Mouyokolo right in front of goal but he scuffed his shot and Friedel pushed the ball over the bar.
Hull’s night took another turn for the worse in the 75th minute when a speedy Villa break ended with Boateng fouling Milner in the area.
Dean had no hesitation in pointing to the spot and Milner easily beat Duke.
HULL: Duke, McShane, Sonko, Mouyokolo, Dawson, Fagan, Cairney (Geovanni 70), Boateng, Kilbane (Olofinjana 84), Bullard, Vennegoor of Hesselink (Altidore 54).
ASTON VILLA: Friedel, Cuellar, Collins, Dunne, Warnock, Downing, Milner, Petrov (Sidwell 84), Ashley Young, Agbonlahor, Carew (Heskey 90).
Referee: Mike Dean (Wirral).