13.11.2015 at 15:00 Vilnius
Referee: P Ardeleanu (CZE)
Lukas Spalvis 23 mins
Simonas Stankevicious 45 mins
Donatas Kazlaukas 73 mins
Conor Wilkinson (43)
Although the hosts had neither scored nor claimed a point in five qualifiers, Noel King's side suffered their wrath in Vilnius by finishing second best and a player light.
Although Conor Wilkinson cancelled out the hosts' opener, Ireland conceded again before the break and a third followed on 73 minutes.
"We'd had good displays in the campaign till now but that was a different team out there tonight," explained King.
"Lithuania probably deserved their win and maybe our players were over-confident after beating them 3-0 at home last month."
On 23 minutes, Donatas Kazlaukas fed Vykintas Slivka on the left and his first-time cross to the far post was brilliantly headed home by Lukas Spalvis.
Wilkinson, however, led the Irish response with Barnsley forward nodding an effort against the crossbar and bringing the best out of Edvinas Gertmonas with a ferocious volley.
There was nothing the Stade Rennais custodian, a senior international, could do about Wilkinson's next attempt two minutes short of the break.
Controlling a left-wing cross from substitute Reece Grego-Cox, he skipped past home captain Justinas Janusevskis on the edge of the box and buried a low strike into the bottom right corner.
Lithuania took less than a minute to regain the lead. When Deimantas Petravicius was allowed break down the right, his cut-back was smashed high into the net by Simonas Stankevicious from 10 yards. Chasing a second leveller against a side content to sit back was a mission Ireland found difficult.
Although Callum O'Dowda was denied by Gertmonas three minutes after the restart with a header that was tipped around the post and Sean Kavanagh fluffed his shot from close range, Lithuania were rarely troubled.
Instead, Ireland's task was put beyond them with 17 minutes left when they gifted their hosts a third. Darragh Lenihan's uncharacteristic error left his defence exposed and Donatas Kazlaukas seized upon the mistake by stroking the ball past Rogers.
To cap an awful night, Kavanagh was sent off in the last minute for a late tackle on Rolandas Baravyykas.
That rules the Fulham man out of Italy's visit in March - a fixture which Ireland need something from to revive their qualification aspirations.
LITHUANIA - E Gertmonas; R Baravyykas, J Janusevskis, J Aleksandravicius, L Cerkaukas; K Silkaitis, V Slivka; D Petravicius, S Stankevicious, D Kazlaukas (D Romanovskij 89).
IRELAND - D Rogers; S Long, D Lenihan, S Griffin, J Connors (R Grego-Cox 18), A Browne, J Byrne (D Connolly 65), J Cullen, C O'Dowda, C Wilkinson (S Maguire 83), S Kavanagh.