Has a College Football game ever ended 54-39?
Exactly once. On November 25, 2016, LSU beat Texas A&M 54-39, and no College Football 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 1820th most common final score out of 2,216 that have ever occurred in College Football. One point away, 55-39 has happened never and 54-40 has happened 1 times.