I don't know if it's ever been specifically stated what he played, but I think it was the rhythm guitar for the last 30 seconds or so of the song.
The story about the end of the song is that they were up late recording and they felt the ending sounded cliche, so at Eric's suggestion they decided to mess the ending up. If you listen around 4:35 the drums go off beat (that's Dean drumming), the bass line gets super repeatetive, and the rhythm guitar goes off key. I think that's Scott playing rhythm at the end there, but I'm not 100% certain.