Egle Stakneviciene scored four of her 10 points at the end of the third quarter to put Lithuania in front for good and on their way to a 67-57 win at Germany.
The triumph sealed a top-two finish for the Lithuanians, who have advanced with Israel from EuroBasket Women qualifying Group A to next year's Final Round in Latvia.
A three-ball by Alexandra Müller had given Germany a 44-42 advantage but Diana Razmaite tied the contest with a jump shot and then Stakneviciene followed with two free throws and a lay-up for a 48-44 advantage.
Razmaite capped the 8-0 run with a basket at the start of the fourth quarter and the Germans got no closer than four points the rest of the way.
Germany finished Group A play with two wins and six defeats.