The game at the Cricket Pitch B of the Moshood Abiola National Stadium, saw Nigeria win the toss and elect to bowl.
Elochukwu Ndububem and Captain Ridwan Kareem did the most damage against the Botswana side, jointly taking out 6 wickets in 11 overs.
The visiting side needed to rely on Karabo Makwatse and Leungo Mosalaesi to put up 36 runs in 25 balls collectively, to see Botswana score 56 runs all out in 24.2 overs.
A very disciplined Nigerian side came on to chase the target, relying only on the partnership between Pam Paul and Selim Salam to finish the game with 58 runs, no loss of wickets in 10.5 overs.
Nigeria will square up against Sierra Leone on Tuesday in their last final group B game.
The News Agency of Nigeria reports that six countries are currently featuring in the qualifiers with the top three teams, to progress to the next stage of the World Cup qualifiers.