Scott Quigley had put Town in-front against his former club, but Chris Holroyd cancelled it out before half-time.
Rodney then poppped up in added time with another fantastic goal - his seventh in 11 matches - to ensure Town ended their home campaign on a high.
The Shaymen were made to work hard for their win, with Sam Johnson pulling off some fine saves, but Halifax dug in for a result that does them great credit after the disappointment of Friday's defeat at Hartlepool.
Luke Young was given far too much space to get a shot away after Wrexham worked a short corner early on, but the effort was blocked before a goalmouth scramble ensued.
Matty Brown, who was magnificent all afternoon, was needed for a couple of important headed clearances from dangerous Wrexham crosses, and then Bobby Grant flashed a left-foot shot over the bar from 20 yards.
Wrexham had settled quicker into the game, although Brown headed a corner straight at Rob Lainton after a quarter of an hour, while James Berrett's shot was blocked from Ryan Gondoh's lay-off as The Shaymen worked their way into the contest.
Loanee Gondoh, one of three changes along with Quigley and Niall Maher, was a decent outlet for Town on the right of a 4-4-2, not always producing an end product but willing to run at players with the ball.
Fellow loanee Quigley has failed to replicate his fine form as a Wrexham loan player of eight goals in 17 games last season, and had only netted once in the same number of appearances for The Shaymen.
But he took his goal superbly to hand Town the lead when Cameron King, who again impressed in midfield, slipped a superb through ball to the left of the box, and Quigley did the rest with an assured finish high into the far corner; his last act before succumbing to injury.
But 10 minutes later, seconds after Wrexham's first shot on target, a free-kick by Luke Summerfield that Johnson tipped behind, Holroyd was left with a tap-in after the resulting corner was nodded down by Jason Oswell.
The comeback was nearly completed moments later but Sam Johnson plucked Grant's curling shot out of the air.
Another fine effort by the dangerous Grant was met by a terrific save by Johnson as Wrexham stirred again.
Town's two in central midfield as opposed to Wrexham's three meant Young and Summerfield had seen plenty of the ball, but they hadn't pressed home that advantage enough. King and Berrett were competing well for the hosts, just not producing the service the likes of Rodney required.
The Halifax striker did reach a long ball just ahead of keeper Rob Lainton at the start of the second-half, but captain Shaun Pearson was well-placed to clear in-front of goal.
That preceded three corners in the first five minutes of the second-half for Town, but the game then developed into a scrappy affair with not enough quality on the ball from either side and possession changing hands too regularly.
Gondoh's effectiveness was waning, and he was taken off, while Rodney and substitute Manny Duku had nothing to feed off.
Wrexham's James Jennings was denied what should have been a goal when his close-ranger header was brilliantly saved by Johnson.
Rodney sprang to life with a burst down the right, and his swirling cross was taken off the head of Duku with a terrific clearing header by Kevin Roberts.
A Duku cross towards Rodney was then well defended, before Joe Skarz produced a crucial tackle to prevent a one-on-one for Wrexham 10 yards out.
Rodney then produced another moment of magic with a sweet low strike with his left-foot that flew across goal.
Hopefully not just something for the Shay fans to remember him by.
Halifax: Johnson, Maher, Clarke, Brown, Skarz, Gondoh (Preston 70), Berrett, King, Kosylo, Rodmey, Quigley (Duku 37). Subs not used: Rowley, Staunton, Freedman.
Scorers: Quigley (29), Rodney (90)
Shots on target: 3
Shots off target: 7Corners: 9
Wrexham: Lainton, Roberts, Pearson, Kennedy, Jennings, Summerfield (Rutherford 67), Young, Oswell (Beavon 67), Wright, Grant, Holroyd (McGlashan 80). Subs not used: Dibble, Carrington.
Scorer: Holroyd (40)
Shots on target: 8
Shots off target: 6Corners: 6
Attendance: 2,577 (1,196)
Referee: Andrew Miller
Town man of the match: Sam Johnson