But it took two late goals to make sure of the points and the game was a lot closer than the scoreline suggests.
Halifax dominated the game early on and deserved to go ahead through Lewis Kileen. Exeter pulled level through Jon Challinor and went ahead after the break through Adam Stansfield.
But Halifax continued to be a danger and Exeter only made sure of the points with a strike from Jamie Mackie in the 89th minute and a second goal from Challinor a minute later.
Exeter preferred Stansfield in attack to Jamie Mackie and Danny Clay replaced Paul Buckle. Halifax gave a full debut to Nicky Gray, son of former Leeds legend Eddie, and welcomed back Ryan Toulson for his first start in more than a year.
The Grecians hadn't lost at home in the league since March. But it was the visitors who had the first chance of the game, Jake Wright slicing a free-kick just past the post from 25 yards in the fourth minute.
Halifax passed the ball around well in the early stages and Toulson scuffed a shot wide after a half cleared corner.
It came as no surprise when the visitors took the lead in the 17th minute. Steve Torpey's neat pass picked out Kileen and the striker unleashed a powerful drive past Martin Rice from a tight angle.
The goal silenced St James' Park but there could be few complaints after Halifax completely dominated the first quarter of the game.
But Exeter were soon on level terms with their first attempt on goal. Andy Taylor's fine corner was met by Challinor who leapt superbly to nod the ball powerfully past Craig Mawson.
Exeter grew in stature after the goal and Stansfield had a shot deflected past the post as they pushed forward.
Suddenly it was a different game and Exeter looked dangerous. They should have taken the lead when Rob Edwards found Stansfield and the striker was denied by Mawson as the goalkeeper rushed off his line. Taylor picked up the rebound and found Clay, whose close-range strike was deflected just wide.
Challinor almost put the Grecians ahead when he exchanged passes with Lee Phillips and struck a powerful shot from 30 yards which was scrambled wide by the outstretched Mawson.
Halifax faded badly as the half wore on. But striker Ryan Sugden was still a threat and only a lunging tackle from Billy Jones denied the striker after a fine run into the box.
Halifax started the second half as they started the first, and had a string of early chances.
Kileen and Danny Forrest both had low shots saved by Rice in the opening minutes. Torpey then shot wide and Forrest had another effort saved by Rice as Halifax threatened to take the lead.
But Exeter weathered the storm and again took control of the game.
Challinor had a low shot saved by Mawson and Phillips shot wide from long range.
At the other end Gray fired wide for the visitors but Halifax again faded badly and allowed Exeter to dominate.
Exeter eventually took the lead with 13 minutes left on the clock. Substitute Mackie flicked the ball out to Jones and when the defender swept in a low cross the ball was slotted home at close range by Stansfield.
Exeter made sure with two late goals. In the 89th minute Challinor put Mackie through and he drilled the ball into the bottom corner. It spilled back out through a hole in the net and was eventually lashed home by Stansfield, but the goal clearly belonged to Mackie.
A minute later Danny Woodards picked out Challinor who lashed the ball home at the far post.