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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Feleipe' Franks, the No. 4 pocket passer in the ESPN 300 and No. 59 player overall, committed to Florida after breaking his verbal pledge to LSU amid the Tigers' coaching uncertainty.