Lithuania had threatened to run away with it early in the second quarter, going on a 15-3 streak to lead 29-11 when Sarunas Jasikevicius played the alley-oop pass for Martynas Pocius to slam home.
But Nigeria rallied and Tony Skinn's free throws cut the gap to 34-27 before the break.
Lithuania's class told in the second half, though, and an 11-2 run gave them a 47-32 lead on Jonas Valanciunas' free throws.
Nigeria went down fighting in the fourth quarter but Lithuania's lead only grew.
Darius Songaila led Lithuania with 12 points while Linas Kleiza had 11 and Rimantas Kaukenas 10.
Ike Diogu and Al-Farouq Aminu had 12 points each for Nigeria while grabbing 10 and 11 rebounds respectively, with Alade Aminu adding 10 points.