Noel King's side were beaten by a Lithuanian side that included seven senior internationals and were well deserving of the three points on the night.
The Irish suffered a blow just before kick-off when Glen Rea was ruled out after a training ground injury was aggravated in the warm-up so Shane Griffin was drafted into the starting line-up.
Lithuania opened the scoring in the 22nd minute when the impressive Lukas Spalvis finished off a counterattack with a looping header to the Irish net.
Seven minutes later Ireland were unlucky not to level in the 29th minute when Conor Wilkinson saw his header from a Jack Byrne corner hit the home crossbar and a defender cleared before Shane Griffin could get to rebound.
Callum O'Dowda had a strike saved in the 33rd minute before keeper Edvinas Gertmonas saved comfortably from a strike by Reece Grego-Cox from outside the box.
Ireland drew level in the 44th minute when Wilkinson produced a brilliant strike from 20 yards that flew past the keeper.
But the Irish were caught cold as they conceded another goal just 60 seconds later with Simonas Stankevicius shooting home from the edge of the box after a break down the right.
One minute into the second half keeper Gertmonas made a crucial save to claw an O'Dowda header to safety after the winger connected with a Sean Kavanagh free-kick.
Despite Ireland's domination early in the second half the home side were always a threat on the break. In the 52th minute Deimantas Petravicius burst in from the right and his low strike was saved by Rogers.
The Lithuanians got a decisive third goal in the 72th minute when a defensive mix-up saw Stankevicius slip through Donatas Kazlauskas and he slot the ball under the advancing keeper Rogers.
Ireland had a decent chance to pull one back in the 85th minute when a clever corner kick routine saw the ball land at the feet of Grego-Cox but he pulled his shot wide across goal.
The disappointing evening was compounded in the 88th minute when Kavanagh was dismissed for a foul on Deimantas Petravičius.
Ireland meet Norway in a friendly game at the RSC, Waterford, on Tuesday
LITHUANIA: Gertmonas, Aleksandravičius, Čerkauskas, Slivka, Šilkaitis, Stankevičius, D. Kazlauskas (Romanovskij 89), Spalvis, Januševskis, Petravičius, Baravykas.
REPUBLIC OF IRELAND: Rogers, Long, Connors (Grego-Cox 18), Griffin, Lenihan, Browne, O'Dowda, Cullen, Wilkinson (Maguire 81), Byrne (Connolly 65), Kavanagh.