Town could have extended their lead even further in the second period, before City scored a late consolation goal.
Huddersfield started confidently and were almost ahead within a minute, as Oliver Norwood's curling effort went inches wide of the post.
Vaughan missed the chance to get his second minutes after that when he couldn't quite reach Novak's header across goal. However, it didn't matter, as the striker was on hand to head in Norwood's free kick on 14 minutes.
He was denied a first-half hat-trick not long after, when he was played through by Novak but Tom Heaton came out on top in the one-on-one situation.
After a scrappy start the second period, it was Huddersfield who scored again with Vaughan completing his hat-trick by getting on the end of yet another cross from his strike partner Novak to head home from close range.
Lewin Nyatanga managed to head in a consolation goal for the already-relegated City, but it wasn't enough to dampen the spirit of Huddersfield, who take a big step towards survival.