The striker, making his first start in eight games following a thigh problem, struck in the 87th minute to help the Terriers avoid a third successive defeat.
After Mark Davies had cancelled out Zat Knight's first-half own goal, Chris Eagles wasted the chance to put his side in front when his 74th-minute penalty was saved by Alex Smithies.
However, the in-form winger looked to have given Bolton, who lost to struggling Ipswich last weekend, the three points six minutes later before Vaughan's late leveller.
It was the hosts who went ahead in the ninth minute when Anthony Gerrard headed Oliver Norwood's corner goalwards and the ball went in off visiting defender Knight.
Town were unfortunate not to double their advantage when Adam Clayton's shot was parried by Adam Bogdan and Lee Novak hit the rebound against the crossbar.
Huddersfield finished the half strongly, with Norwood curling a free-kick from the edge of the area just wide before Bogdan had to backtrack quickly to tip over Jack Hunt's teasing cross.
Bolton came out firing in the second half and Knight almost made up for his earlier error but his header was off target, before Lee Chung-yong shot narrowly wide from an acute angle. Wanderers' pressure told in the 69th minute when Mark Davies picked up a pass from Eagles and side-footed home from 12 yards.
Eagles missed a glorious opportunity to put his side into the lead five minutes later as his penalty was tipped onto the post by Smithies after Paul Dixon fouled Sam Ricketts in the area. However, the former Manchester United winger made amends shortly afterwards when he found the net from 12 yards.
But Vaughan secured a point for Simon Grayson's outfit three minutes from time, shooting into the bottom corner.