The Pools are the form team in the division and were good value for another victory.
They were set on their way after 32 minutes as James Poole was tripped in the penalty area by Alan Bennett and Simon Walton smashed in from 12 yards.
Scott Flinders made a fine stop from Michael Smith to keep the lead intact a minute later and the visitors should have levelled on half-time, but Bennett sent a free header over from close range.
However, the Dons were level from a penalty of their own on 66 minutes, when Jack Baldwin bundled George Porter over and Harry Pell sent Flinders the wrong way.
It was only six minutes before Pools regained the lead, though, with Walton's pass picking out Luke James, whose looping header sailed over keeper Ross Worner into the net.
And the points were sealed on 83 minutes as Matty Dolan's low shot from 25 yards had too much power for Worner, who couldn't keep it out.