After a goalless first half, the hosts took the lead on the hour mark when Jon Russell was allowed to receive a throw and lob keeper James Shea to open the scoring.
James Bree was then clipped inside the area on 70 minutes for a penalty that top scorer Elijah Adebayo put against the outside of the post, before Terriers sub Naby Sarr was left unmarked to head home a corner with a minute to go.
Speaking afterwards, Jones said: “It hinges on us not defending two situations because they didn’t have to work hard (to score).
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"We were excellent I thought in terms of defensive shape, in terms of everything we did.
"We were bold, we were brave, we moved the ball, second half I thought we were really good, stepped on to the front foot, but they took a throw-in, he walked off the back of someone and then looped the ball in the box which has gone in.
"He didn’t try that, so an element of luck and then late on, Naby Sarr comes on, he’s six foot seven and no-one picks him up and you think, ‘come on.’
"So two naive bits of defending and that’s cost us and then been further compounded by a penalty miss when we were really, really in the ascendancy.
"That has changed the direction of the game, but that’s what Championship football is.”