The visitors, just three points above the npower Championship drop zone coming into this clash, hit the ground running and took the lead after just two minutes thanks to the Norwich loan striker.
The 24-year-old then scored two simple headers to make it 13 for the season before City grabbed a last-gasp consolation through Lewin Nyatanga.
The pre-match talk surrounded the absence of in-form striker Jermaine Beckford, but Vaughan stepped up to the plate in the perfect fashion, slamming home Lee Novak's cross.
Huddersfield had not won successive matches since October but they looked set to break that unwanted run in the 13th minute when Vaughan grabbed his second of the afternoon.
The striker rose unmarked to nod home Oliver Norwood's free-kick from the left flank five yards out to delight the 1,546 travelling fans and give Mark Robins' men some breathing space.
Just seven minutes later the former Everton man was denied a 17-minute hat-trick by a superb Heaton save after the striker was sent through by Novak's clever pass.
Albert Adomah, City's man of the match in the 0-0 draw with Hull last weekend, almost gifted Novak the ball on the hour mark when his successful back pass to Heaton went wrong.
But Huddersfield only had to wait three minutes for another goal, Novak crossing from the right wing for Vaughan to complete his hat-trick with a simple header from close range to wrap up the points.
Sean O'Driscoll's men did grab a consolation in the 90th minute, Wales defender Nyatanga heading in at the far post.