The Gills looked the brighter side in the opening minutes and visitors goalkeeper Arran Lee-Barrett had to be on his toes.
He saved well from Delroy Facey twice and also kept out a wicked curling cross from the right by Dennis Oli as it threatened to sneak under the crossbar.
But Hartlepool began to get their game together and, after Antony Sweeney sent a shot a foot over an open goal when he should have scored and had another goal disallowed for a foul deep in the area, two home goals in five minutes put them in control.
First, on 21 minutes, Andy Monkhouse almost had his back to goal when a poor Gillingham clearance came his way and from 25 yards he swung his left foot to curl a shot into the top corner.
Then, on 26 minutes, came a brilliant solo goal from Joel Porter, who beat his marker in his own half, beat another defender on the fringe of the penalty area and finished with a perfect chip over keeper Derek Stillie.
Midway through the second half, Gillingham were pressing for a goal and got a penalty when Lee-Barrett fouled Simeon Jackson in the area, but the keeper made amends with a brilliant save from Adam Miller's spot-kick.
Four minutes later Hartlepool made it safe when Sam Collins powered in a header from Jamie McCunnie's right-wing corner.
And McCunnie wrapped it all up in added time when he curled his free-kick from the left inside the far corner.
With just one win in 11 games, Gillingham are deep in trouble, but Hartlepool look a lot safer after two wins in a week.