Martin O'Neill rested a host of first team regulars as he did against the Slovakian minnows at Villa Park and again paid the price. Villa's second string were comfortably brushed aside by Martin Jol's powerful and tricky outfit.
Croatian duo Mladen Petric and Ivica Olic destroyed a sloppy Villa side, who managed a consolation through bright spark Nathan Delfouneso.
Petric grabbed the first and Olic put the home side out of sight with a brace before Delfouneso struck.
Steve Sidwell was dismissed late on to compound a night of misery for all involved with the Claret and Blue.
Travelling fans were left dismayed prior to kick off as ineffective midfielder Moustapha Salifou and shaky defender Zat Knight were chosen to taken on a full strength Hamburg side.
Although supporters realise that the Premier League is top of the priority list, they will clearly be unhappy that they have spent money to see a 2-1 defeat against Zilina and now a 3-1 reverse on the continent.
Villa now face a group topper in the knock-out stages and will be hoping to avoid the likes of CSKA Moscow and Everton's conquerors Standard Liege.
The draw takes place in Nyon on Friday and O'Neill will now be hoping that it is kind to his men after being quoted as saying he didn't care where Villa finish in the group.
Theoretically, Villa may have been better finishing third as Ajax, who ended the group in second spot, will face a Champions League drop-out.
Ninja
However, pride is important for any fan or player and Villa lacked that vital quality as they struggled to cope with a Hamburg onslaught.
Petric struck on just 18 minutes as Carlos Cuellar and Luke Young stood off the striker, who took down a raking through ball and volleyed past Brad Guzan.
Olic then got in on the act as Cuellar was again at fault. The Spanish defender failed to get close enough to the diminutive Croat and he was able to divert a diving header past the hapless Guzan.
There was no let up for Villa as they emerged after half time and Olic quickly doubled his personal tally on 57 minutes. The striker held off a weak challenge from the calamitous Cuellar and guided the ball home.
Villa then began to improve as Hamburg relaxed and Delfouneso guided in Moustapha Salifou's cross to add a little respectability to the score line.
Youngster Barry Bannan was introduced for Villa and he provided a some impetus. The Scot looked busy in midfield and was one of the few positives on the night.
Sidwell had less of a positive influence, though, and the ginger ninja was sent off for a second bookable offence just before the end of match.
The midfielder would have had a mood which mirrored that of the travelling support, who were entitled to feel like they had been mugged on foreign soil.
To look at the positives, Villa are now through and they will definitely need to play their strongest side if they are to progress to the latter stages.
There is no reason for Martin Laursen and Co to fear anyone in the competition but on this evidence Villa will have to steer clear of New Year injuries if they are to reach the promised land of Istanbul.