Gabriele Sulske ignited a 5-3 spark with 3:53 left in the game for a 19-15 lead for Lithuania.
Tantoy Ferrer was able to score a point with eight seconds remaining but Kamile Nacickaite iced both her free throws with 5.7 ticks left to end the game.
Nacickaite was the only player on both sides to reach double digits with 11 points while Sulske had five points for the Lithuanians.
Tantoy Ferrer scored three points for Gilas Women as they are relegated to the loser’s final for the last World Cup slot against the Singaporeans at press time.
The Philippines narrowly escaped Singapore, 21-19, in their recent match last Saturday in the preliminary round.