Lithuania led the contest wire-to-wire, finishing with a 42-34 point advantage in the paint while hitting 7-14 from the three-point line.
The Australians were led by Joe Ingles (16 points, four rebounds, two steals) who completed a successful reunion with the team after staying back home for the birth of his twins at the start of the tour.
Aron Baynes also stood out with 14 points to go with seven boards while Patty Mills added 11 points and Australia's bench out-scored their opposition 37-22.
However, they struggled to connect from distance overall, shooting only 4-19 as a team.
A high-tempo start from both sides saw Lithuania jump out to an early lead although the work of Mills and Baynes kept the Australians in the contest before Ingles saw his first court time of the tour mid-way through the opening period.
He looked to ignite Australia with back-to-back three-point plays in the second quarter, cutting a double-digit lead down to eight before Lithuania were able to answer with a couple of long range bombs from Marius Grigonis.
Cameron Bairstow then put his stamp on the game with four quick points late in the half to cut the margin to 32-41 at the main break.
Baynes' physical battle with fellow NBA player Jonas Valanciunas continued into the third quarter with the two big forwards looking to assert their presence in the paint.
However, Valanciunas had more help under the rim and second chance points helped Lithuania extend their lead to a game-high 17 points.
The Aussies' full-court press aimed to eat into that deficit with Damian Martin and Kevin Lisch (five points, one assist) providing great pressure while Matthew Dellavedova (two points, four assists) pushed the pace offensively but the margin proved too much to overcome as Australia dropped their second straight game for the tour.
Find the full box score for the game here.
The Australian men's final warm-up game will now be played at 1am AEST Monday morning against either China or Brazil, depending on the final results of the Euro tournament.
Don't forget you can also catch the Aussie women in their last warm-up game at 6am AEST Monday morning as they face the Americans at Madison Square Garden.
USA Basketball will be providing a livestream on their Facebook page and it will also be shown on ESPN Australia/NZ.