The NNL and the NAL faced each other in the Negro World Series at the end of the season to determine an overall champion.
Champ
CLE
1945 NAL Champion Cleveland Buckeyes
z: best record, c: conference winner, y: division winner, w: wildcard, x: clinched playoff spot

Negro World Series

Best of 7-game series
Date    OpponentResultScoreSeries
9/13vs HomesteadW  2-1 1-0
???vs HomesteadW  4-2 2-0
???at HomesteadW  4-0 3-0
9/20at HomesteadW  5-0 4-0