Basle brush off battling Boro
Steve McClaren's side were a match for their hosts - who boast a Champions League victory over Celtic and draws against both Manchester United and Liverpool in the recent past - for much of the game.
However, they were undone inside three devastating minutes at the end of the first half as Argentinian midfielder Matias Delgado claimed his seventh goal in the competition and then David Degan added a second on the stroke of half-time.
Boro came close to pulling one back when Chris Riggott's header hit the bar. But Delgado also saw a free-kick clip the woodwork, and Riggott hacked another effort off the line.
Fighting in the crowd at half-time marred the evening for the 1,400 or so travelling supporters, but the biggest trouble for Boro came on the pitch.
Boro's game plan was much as it had been against both Stuttgart and Roma in the previous rounds - the pursuit of a potentially invaluable away goal and a clean sheet.
For 43 minutes, they were at least halfway there as the Swiss side struggled to break them down despite left-back Franck Queudrue having his hands full with midfielder Degen.
Just as it looked as though they had safely negotiated the opening 45 minutes, disaster struck. Goalkeeper Mark Schwarzer had earlier had to keep out a well-struck drive from defender Boris Smiljanic, but he was to be defeated by both danger man Delgado and the pitch.
There seemed to be little to concern the Australian when the South American received the ball from Bruno Berner on the left touchline. However, he cut inside Ray Parlour and unleashed a dipping right-foot shot which reared up off the rain-sodden turf and flew over the helpless goalkeeper.
Schwarzer was still dusting himself down when striker Eduardo played the ball in behind Emanuel Pogatetz for Degan to slide a second beyond the hopelessly exposed goalkeeper.
The visitors could barely believe what had happened as they trudged off the pitch at the break.
Boro went close within four minutes of the restart when Hasselbaink directed a header towards Zuberbuhler's bottom left corner, and the goalkeeper was at full stretch to turn the ball away.
But he was beaten from the resulting corner when Riggott powered in a header from Mendieta's cross, only for his effort to clip the crossbar and fly to safety.
Basle looked more likely to add to their tally than Boro did to grab a lifeline as the clock ran down. Ehiogu might have done just that with a minute remaining but saw his header from a Downing corner saved on the line.
It was a dejected visiting side which left the pitch - knowing that, while they are still in the tie with George Boateng and Lee Cattermole available after suspension, they have a mountain to climb.
: Zuberbuhler, Majstorovic, Berner, Smiljanic, Sterjovski (Chipperfield 64), Ba, Delgado, Degen, Zanni, Eduardo Da Silva, Petric (Ergic 85).
: Schwarzer, Parnaby, Riggott, Pogatetz (Ehiogu 68), Queudrue, Mendieta (Rochemback 74), Parlour, Doriva, Downing, Hasselbaink (Yakubu 74), Viduka.
: Domenico Messina (Italy),
: UEFA Cup quarter-final first leg: Levski Sofia 1 Schalke 3, Rapid Bucharest 1 Steaua Bucharest 1, Seville 4 Zenit St Petersburg 1. International friendlies: Japan 1 Ecuador 0, Mexico 2 Paraguay 1.
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