Has an AFL game ever ended 54-39?
Exactly once. On June 5, 1905, Essendon beat St Kilda 54-39, and no AFL game before or since has ended that way. When it happened it was a scorigami, the first 54-39 in league history.
That makes 54-39 the 3836th most common final score out of 6,607 that have ever occurred in AFL. One point away, 55-39 has happened 3 times and 54-40 has happened 4 times.