Stephen Kenny named five players with Cork origins in the starting lineup, the most from any county on the International side to date. Kenny made six changes from the squad that drew with Belgium on Saturday, with Will Keane making his first start for his country.
The home side had the opening chance of the evening, with Ryan Manning going close after the ball was cleared to him from a corner, but his effort went just past of Dziugas Bartkus' post. Chiedozie Ogbene put the ball in the back of the net shortly later, but the goal was ruled out owing to offside.
Conor Hourihane appeared to have given Ireland the lead early in the second half with a low shot that beat Bartkus at his near post, but the flag was raised for offside because two Ireland players were in an offside position.
In a rare attacking spell for the visitors, Lithuania had two chances in close succession. A shot by Edgaras Utkus was deflected for a corner, and Rolandas Baravykas missed the target with a strong effort. Ireland had once again a goal disallowed for offside after James McClean's cross to Ogbene at the back post saw his goal ruled out.
Troy Parrott, a second-half substitution, curled a shot from the edge of the box go just wide of Bartkus' far post. John Egan was the next player to try to beat the Lithuanian goalkeeper, but his header from a Parrott cross was well saved.
With a superb attempt, Parrott appeared to have clinched the tie for the home side, only for Bartkus to deny him with a great stop sending the ball over the bar. Scott Hogan had the ball in the net for Ireland for the fourth time, but he had wandered into an offside position.
With barely seconds remaining in the game, Troy Parrott grabbed the ball on the edge of the box and struck a magnificent half volley to ultimately beat Bartkus and Lithuania's resistance and give Kenny's men the deserved victory.
Republic of Ireland: Caoimhin Kelleher, Ryan Manning, John Egan, Callum Robinson (Scott Hogan 77), Conor Hourihane, Will Keane (Troy Parrott, 62), Matt Doherty, Nathan Collins, Alan Browne (Jeff Hendrick 81), Dara O’Shea (James McClean 62), Chiedozie Ogbene (Jason Knight 81).
Subs not used: James Talbot, Max O’Leary, Seamus Coleman, Shane Duffy, Josh Cullen, Mark Sykes, Jayson Molumby.
Lithuania: Dziugas Bartkus, Linas Klimavicius, Titas Milasius (Donatas Kazlauskas 46), Edgars Utkus, Benas Satkus, Egidijus Vaitkunas, Fedor Cernych (Gratas Sirgedas 86), Vykintas Slivka, Justas Lasiskas (Pijus Sirvys 82), Augustinas Klimavicius (Ignas Kruzikas 60), Rolandas Baravykas.
Subs not used: Evvinas Gertmonas (GK), Ignas Plukas, Eligijus Jankauskas, Saulius Mikoliunas, Ovidijus Verbickas, Armandas Kucys.
Referee: Jonathan Lardot (BEL)
Carlsberg Player of the Match: Nathan Collins (IRL)