A lone header from David Mirfin from Adnan Ahmed's corner was enough to settle it and send the Terriers in with a lead at half time.
It could have been so different if Wrexham had done better in front of goal but they wasted chances with wayward shooting and poor finishing.
Live wire Carlos Edwards went nearest with a sharp drive that Paul Rachubka tipped over his bar in the first minute.
Chris Llewellyn had the next chance but his tame header from Juan Ugarte's cross was easily saved.
Llewellyn missed a completely open goal when Danny Williams and Ugarte combined to put him through.
Then Edwards beat two men and shot wide before Llewellyn set up Ugarte for another opening but Danny Adams came to Huddersfield's rescue by clearing off the line.
Ahmed tried a long shot early on and Chris Brandon followed up with a 40-yard effort that went straight at goalkeeper Ben Foster.
Brandon was equally out of luck with his next angled shot which Foster saved with ease.
Andy Booth flicked on a goal kick to set up Brandon only for him to shoot wide from the edge of the penalty area.
Andy Holdsworth overlapped from the back to try a long shot over the top before Mirfin put Huddersfield into lead.
The game had an end of season look about it with nothing to play for and both sides made substitutions without any great change to the match.
Substitute Mark Jones angled a 20-yard shot wide and Hector Sam also missed the only chance of his afternoon.
The game was held up briefly when about 20 fans invaded the pitch, causing match referee Lee Probert to call the players into the middle until the police restored order.
With time running out Huddersfield showed more enterprise and Pawel Abbott might have done better with a tame shot that hit the foot of a post and bounced away.