Scott had scoring strikes of 5 yards to LaVon Brazill, 42 yards to Taylor Price and 63 yards to Terrence McRae for the Bobcats (2-1). He finished 14-for-27.
Price had nine catches for 135 yards and McRae had three receptions for 93 yards.
Errik Ejike started Ohio's scoring with his first career interception and touchdown, a 23-yarder in the first quarter.
Chris Garrett had 91 yards on 15 carries for the Bobcats.
Greg Francis scored the Mustangs' only touchdown on a 60-yard interception return of a Tyler Tettleton pass with 2:36 left in the game.
Cal Poly (1-1) rushed for 239 yards, but had only 12 passing yards as Tony Smith was 1-for-11 with two interceptions.