Monsoon conditions were the backdrop to a demanding second half which the referee boldly allowed to run its course despite a rapidly deteriorating pitch.
Had the kick-off been 15 minutes later, the match would surely have been abandoned as the storm reached its height and flooded sections of the ground.
With the elements behind them, United had the better of the first half and will regret missing a couple of decent chances, notably when Craig Lindfield worked an opening but saw his shot from a tight angle pass outside the far post.
The Mancunians also hit the bar in a goalmouth scramble as the half drew to a close.
But it would have been a different story if Jason Walker had not missed a golden chance early in the game.
Marcus Carver broke at speed down the right and squared a lovely pass to the unmarked Walker who from 10 yards fired wildly over the bar.
Chorley took a firmer grip on proceedings after the break and little was seen of United in attack, with Matt Urwin largely untroubled in the home goal.
But it took time to produce the knockout blow. Good work on the right by Walker teed up a straightforward finish for Carver six yards out, but he could not squeeze the ball beyond keeper Lloyd Allinson, who raced off his line to smother the shot.
Man-of-the-match Nick Haughton’s wizardry on the ball stood out time and again amid the deluge and it was fitting that he should score the winning goal.
After a bout of ping-ping in the United box in the 72nd minute, Haughton nipped in to drive the ball into the back of the net from short range.
United could not muster a serious counter against a solid home defence and only a superb save by Allinson prevented a second Chorley goal in the closing minutes.
Josh Wilson let fly from 30 yards and his shot was heading for the top corner until Allinson arched himself athletically to tip the ball over the bar.
Moments before that, the visitors were reduced to 10 men, Zac Corbett receiving a straight red card for violent conduct in a brief melee following a foul on Matty Hughes.
The win lifts the Magpies into sixth place and earned the players the praise of a delighted Jansen, who pointed to, ‘A real show of character’ in the conditions and in view of the long trek to Boston in midweek.
CHORLEY: Urwin, Challoner, Blakeman, Teague, Leather, Anson (Charnock 89), Haughton (Hughes 81), Wilson, Carver, Walker (O’Keefe 67), Cottrell.
Subs (not used): Azam, Jarvis.