Hughes rushed for 93 yards on 21 carries for Rhode Island (3-9, 1-7 Colonial Athletic Association), scoring on an 11-yard run early in the second half.
Ferrer rushed 10 times for 71 yards and scored on a 3-yard TD run with just over two minutes remaining in the game.
John Griffin scored two touchdowns and had 110 yards rushing on 18 carries for Northeastern (2-10, 1-7 CAA).
Rhode Island's Derek Cassidy was 13-of-22 for 157 passing yards, while kicker Louis Feinstein had three field goals.
Northeastern's Anthony Orio was just 5-of-17 for 47 yards and an interception.
Northeastern led 14-13 at halftime.