Kevin Kampl hit the target with two minutes remaining to settle an engaging encounter in Siauliai, where Slovenia took all three points to make the best of starts in 2013 UEFA European Under-21 Championship qualifying Group 2.
Slovenia ended the game as they had begun it, by dominating their hosts, but there was much to admire from a Lithuania side able to pose the visitors numerous problems. They proved especially menacing after half-time, only for Kampl to race clear as the clock ticked down and bury the ball inside the far corner from outside the area.
The opening game in the section swung back and forth throughout, with Slovenia quickest out of the blocks before the home side threatened to break the deadlock on 22 minutes. Only a fine double save from Jan Oblak kept the match goalless as Tadas Eliošius was denied from point-blank range before Arminas Vaskela had a shot turned over.
René Krhin and Rajko Rep conjured efforts at the other end, but Lithuania came out even stronger after the interval, with Oblak again impressive to thwart Audrius Brokas. Slovenia were struggling to escape from their own half, yet they gradually began creating chances again, substitute Matic Fink shooting wide and Robert Berić unable to beat Aivaras Brazinskas from close range before Kampl's late breakthrough.
The match-winner was subsequently dismissed and will therefore miss his side's next qualifier in Finland on 10 August. Lithuania will chase their first points at home against Malta on Tuesday.