The 22-year-old, on loan from Cardiff, drilled home hard and low into the bottom right corner from Lee Chung-Yong's cross following a corner.
The goal, in the second minute of stoppage-time, stretches improving Bolton's unbeaten away record to five matches.
Wanderers had earlier survived two scares when skipper Jay Spearing cleared efforts off the line in either half.
South Korean Lee missed a first-half sitter in a contest that seemed destined to be end in a draw.
He hit the post when unmarked from close range on 15 minutes from Alan Hutton's byline pull-back. Huddersfield goalkeeper Alex Smithies was rooted to the spot as Neil Danns put Hutton in on the overlap down the left to pick Lee out.
The Terriers, now without a win in seven games, hit the woodwork through former Bolton winger Danny Ward, who lashed a 25-yard drive onto the top of the bar in the 11th minutes, with goalkeeper Adam Bogdan appearing to get a faint touch.
Huddersfield also went close in the 24th minute when Oscar Gobern had a header from an Adam Hammill corner cleared off the line by Spearing.
Other first half chances followed for Ward, striker Nahki Wells and Hammill, who went close with a chip, before Town nearly shot themselves in the foot.
A weak attempted clearance from Smithies put Peter Clarke in all sorts of trouble on his 500th career start. The home skipper was robbed by Lee, who then tumbled in the box as Clarke tried to recover - although appeals for a penalty were waved away.
At the other end Bogdan got down low at his near post to parry a Gobern header from a Hammill corner in first half stoppage-time.
Both sides traded chances after the break, with Liam Trotter setting up Lukas Jutkiewicz in the 64th minute. The striker, who failed to score in seven games on loan at Huddersfield from Everton in 2009, also drew a good save from Smithies in the 72nd minute.
In between, Ward, who cost the hosts £1million from Bolton three years ago, forced the Hungarian to parry his 20-yard rocket.
Bogdan again did well in tipping over a Ward header from a Tommy Smith cross with 13 minutes remaining after the full-back beat Tim Ream down the right flank. Ream was still wearing a protective face mask having suffered a broken nose against QPR in January.
Danns, who had a loan spell at Huddersfield last season, tested Smithies with a long-range free-kick eight minutes from time.
There was late controversy when Bolton were again denied a penalty after another Smithies blunder. He raced out to collect a loose ball but slipped and then appeared to pull down another former Terriers loanee, substitute Jermaine Beckford.
No foul was given and the game seemed destined to end 0-0 - until Mason popped up unmarked in the box to sweep home his fifth goal of the season.