A bizarre goal by Vetra Vilnius midfielder Nerijus Vasiliauskas after 61 minutes ended Hibs' Intertoto Cup campaign almost before it had begun.
Vetra celebrate their winning goal
Vasiliauskas put pressure on keeper Alistair Brown as he tried to deal with a spinning ball under the bar and got the vital touch virtually on the line.
Hibs were unable to find a response and it is the Lithuanian side who will progress to the next round.
Tony Mowbray's side must now rethink their pre-season plans.
It could have been different if, within the opening two minutes, Hibs had taken their chances but first debutant Sam Morrow and then strike partner Garry O'Connor were denied by home keeper Marius Poskus, who saved the latter's effort from close range.
Hibs poured men forward in search of the goal they required but Poskus was in inspired form.
The Scots were finding it difficult to gain the upper-hand but 10 minutes from
the break they went close to an opener.
Scott Brown set up Steven Whittaker on the right and the full-back's cross was
headed back across goal by O'Connor.
Alen Orman stole in front of his marker but Poskus flung himself at the Bosnian's acrobatic scissors-kick and tipped his shot over.
After the break it was the home side who always looked the most likely to find
the breakthrough, however, and it finally came via Vasiliauskas' goal.
Vetra Vilnius: Poskus, Grudzinskas, Sasnauskas, Raliukonis,
Zudys, Beaud, Rimkus, Butrimavicius, Sernas, Vasiliauskas,
Subs: Merkelis, Kontautas, Kijanskas, Vaineikis,
Litvinas, Stonkus, Mizigurskis.
Hibernian: Alistair Brown, Whittaker, Alan Reid, Caldwell,
Murdock, Nicol, Scott Brown, Brebner, Orman, O'Connor, Morrow.
Subs: Andrew Reid, Smith, Glass, McManus, McDonald, Shields,
Referee: Kryzysztof Slupik (Poland)