Vaughan kept his composure to steer home the winner from inside the penalty area after Leeds substitute Aidy White had cancelled out Neil Danns' opener for the visitors early in the second half.
It was a welcome victory for Huddersfield, beaten 4-2 by Leeds at the John Smith's Stadium in December, and lifted them eight points clear of the relegation zone.
Leeds' outside play-off chances appear to be fading fast as they slipped to their first home defeat since early February. They still trail sixth-placed Nottingham Forest by four points, having played a game more than all their rivals.
Jermaine Easter scored with his first touch and Shane Lowry hit a screamer as FA Cup semi-finalists Millwall beat Charlton 2-0.
Easter, signed on loan from Crystal Palace 48 hours earlier, came on as a 57th-minute substitute and within 60 seconds had fired the Lions ahead.
And defender Lowry made it an unhappy Valley for Charlton again when he rifled in a stunning 35-yard free-kick six minutes later.
Millwall this week secured a Wembley meeting with Wigan next month after sinking Blackburn in their quarter-final replay.
But they have taken their eye off the ball in the league since embarking on their cup run, losing seven of their last eight matches.
However, they returned to the day job in style to secure a valuable three points while condemning their south London rivals to a ninth home defeat of the season.
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- Aidy White