Has an AFL game ever ended 49-46?
Exactly once. On April 30, 2010, St Kilda beat Footscray 49-46, and no AFL game before or since has ended that way. When it happened it was a scorigami, the first 49-46 in league history.
That makes 49-46 the 3836th most common final score out of 6,607 that have ever occurred in AFL. One point away, 50-46 has happened 1 times and 49-47 has happened 4 times.