Andy Robinson's 79th-minute penalty sent Rovers on their way to a first win in four and means they leapfrog Sheffield United and Stevenage at the summit.
Managerless Pool, watched by prospective boss Phil Brown, remain bottom after making it 15 games without a win.
After a quiet first half, Pools should have been ahead just 14 seconds into the second, Jon Franks put in on goal, but keeper Owain Fon Williams saved well.
Home goalkeeper Scott Flinders then made three impressive stops to deny Andy Robinson, Adam McGurk and James Wallace before he was beaten. Hartley tripped Wallace in the area and Robinson made no mistake from the spot.
And in injury time, substitute Cole Stockton ran across the Pools defence and curled a fine effort around Flinders.