Scott Quigley fired Halifax ahead before limping off with a hamstring injury before half time
Devante Rodney scored in second half stoppage time at The Shay to end Wrexham's hopes of a top three National League finish.
Ex-Dragon Scott Quigley fired Halifax ahead before Chris Holroyd equalised from a corner prior to the interval.
Wrexham upped the pace after the break, but goalkeeper Sam Johnson kept out Akil Wright's header.
Kevin Roberts twice denied Rodney before he fired in his seventh goal in 11 games to send Wrexham down to fifth.
Bryan Hughes' men can now finish no higher than fourth in the National League.
Wrexham manager Bryan Hughes told BBC Sport Wales:
"I want to go unbeaten now until the last game of the season.
"From our point of view we want to go up. We gave ourselves a chance of top three, but this result decides our fate.
"Wherever we finish, that is what we will deserved and now we get our first go in the play-offs for six years.
"It is a positive not a negative and we want to galvanise the whole town and get everyone behind us."
