Has an AFL game ever ended 53-39?
Exactly once. On June 28, 1913, Fitzroy beat St Kilda 53-39, and no AFL game before or since has ended that way. When it happened it was a scorigami, the first 53-39 in league history.
That makes 53-39 the 3836th most common final score out of 6,607 that have ever occurred in AFL. One point away, 54-39 has happened 1 times and 53-40 has happened never.