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, 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.
Adam Clayton tried his luck from distance early on, but Adam Bogdan was equal to the former Leeds midfielder's 30-yard effort.
The Trotters responded and dangerman Eagles pulled the ball back only for Keith Andrews to scuff a shot into the hands of Smithies, who then had to keep out an Eagles 25-yard drive after Peter Clarke gave away possession.
But 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.
Bolton almost levelled up three minutes later when Andrews fired narrowly over after Mark Davies saw his effort blocked.
However, Town were unfortunate not to double their advantage when Clayton's shot was parried by Bogdan and Lee Novak hit the rebound against the crossbar.
Huddersfield had to be alert at the back to clear a Sam Ricketts header, while at the other end Chris Atkinson sliced a half-volley over the top from 25 yards.
Town 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.
In the 52nd minute, referee Eddie Ilderton waved away Bolton's appeals for a penalty when Kevin Davies was bundled over in the box.
Kevin Davies was then played in by Lee, although the former England striker's shot whistled past the post.
Bolton's 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 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.