Rimantas Kaukenas finished with 10 points for Lithuania, which bounced back from an opening loss to Argentina. Nigeria fell to 1-1 after opening the tournament with a win over Tunisia.
Lithuania has a long basketball pedigree that includes three Olympic bronze medals, while Nigeria is making its first Olympic appearance in men's basketball.
Nigeria shot just 24 percent from the field and made only one of its 16 three-point attempts.
Lithuania led 34-27 at halftime and steadily increased its margin throughout the third quarter.
Al-Farouq Aminu of the New Orleans Hornets and Ike Diogu had double-doubles for Nigeria. Aminu had 12 points and 11 rebounds; Diogo finished with 12 points and 10 rebounds.