Has a College Football game ever ended 47-39?
Exactly once. On September 6, 2014, Army beat Buffalo 47-39, and no College Football game before or since has ended that way. When it happened it was a scorigami, the first 47-39 in league history.
That makes 47-39 the 1820th most common final score out of 2,216 that have ever occurred in College Football. One point away, 48-39 has happened 2 times and 47-40 has happened 3 times.