Lafayette trailed 10-7 before Andrew Shoop's 10-yard touchdown pass to Ross gave Lafayette its first lead of the game, 14-10, with 3:58 left in the third quarter.
Ross tallied eight receptions for 105 yards. Shoop, who posted 243 yards and two touchdowns on 20 of 33 passing, moved into eighth place all-time for career passing yards and passing touchdowns at Lafayette.
Yale (1-4) attempted to rally, but after the Bulldogs turned the ball over on downs, Scheuerman capped off a 7-play, 78-yard Lafayette drive with a 2-yard touchdown run.
The Leopards, who picked off Yale's Eric Williams four times, have intercepted 15 through six games.
Tyler Varga led Yale with 100 yards rushing.
Lafayette improved to 4-2, equaling its win total from 2011.
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With so much uncertainty at offensive tackle, the Boilermakers will be counting on newcomer Jalen Neal to make an immediate impact.
David Sills, who once committed to Lane Kiffin at USC in seventh grade, is leaving West Virginia to purse his dreams of playing quarterback.
Alleged 1998 rape victim Brenda Tracy said she left Lincoln, Nebraska, with an advocate for her cause in football coach Mike Riley.
There are plenty of questions surrounding Oregon State's offensive trio, but with some consistency this group should rank higher by season's end.
Ole Miss will get a chance to prove itself in the early going when it faces Dalvin Cook and a loaded Florida State team in Week 1.