Has an AFL game ever ended 39-31?
Exactly once. On June 23, 1900, Geelong beat Carlton 39-31, and no AFL game before or since has ended that way. When it happened it was a scorigami, the first 39-31 in league history.
That makes 39-31 the 3836th most common final score out of 6,607 that have ever occurred in AFL. One point away, 40-31 has happened 1 times and 39-32 has happened never.