Has an AFL game ever ended 46-39?
Exactly once. On June 29, 1907, Geelong beat Carlton 46-39, and no AFL game before or since has ended that way. When it happened it was a scorigami, the first 46-39 in league history.
That makes 46-39 the 3836th most common final score out of 6,607 that have ever occurred in AFL. One point away, 47-39 has happened 2 times and 46-40 has happened 3 times.