The home team were coasting, 2-0 up with an hour gone, but Macclesfield battled their way back to level the game, only to be beaten three minutes from time when skipper David Morley deflected the ball into his own net.
Hartlepool started brightly and Antony Sweeney had a second-minute shot deflected wide for a corner, while a minute later Eifion Williams' low shot was tipped round the post by Tommy Lee.
Macclesfield seemed to have contained the home attack when Pools suddenly took the lead on 26 minutes. Williams did well to make space for himself on the left before curling over a cross to the far post, where James Brown looped his header into the far corner over stranded keeper Lee.
But the Silkmen didn't panic and, though they had to defend for most of the time, they did break when they could, and Colin Heath posed problems when he ran at the home defence. He did not create any real chances until first-half added time when he crossed low from the left and John Murphy stabbed his close-range shot wide under pressure from Ben Clark.
The home team stayed on top in the second half, but Macc worked hard to limit their chances and might equalised on the hour, but Alan Navarro's finish at the end of a good move lacked power and Dimi Konstantopoulos saved without too much trouble.
Hartlepool soon went to the other end to double their lead, Sweeney racing clear on the left and crossing low for Richie Barker to force in a close-range finish.
That was the signal for Macc to fight back, and Murphy hit the home post with keeper Konstantopoulos way off his line on 63 minutes. But they got the goal they deserved on 65 minutes when their first corner of the match was not cleared properly and the ball was played into the path of Justin Hadfield, who hit the net with a screamer from 25 yards.
The visitors were level on 70 minutes after their second corner wasn't cleared and John Miles blasted a shot through the crowd, the referee ruling it had crossed the line before being hacked clear.
But Hartlepool won the game and extended their unbeaten run to 17 games when a Humphreys' free-kick on 87 minutes hammered against the bar and as it came out, it hit Morley and rolled agonisingly into his own net.