The 34-year-old striker placed a precise side-footed volley into the corner of the net early on to lift the Dons to within two points of top spot and leave hapless Pools without a win in 21 games.
Milton Keynes dominated the first half and the unmarked Lowe put them ahead on the quarter-of-an-hour mark, tucking Darren Potter's cross past Scott Flinders as the Pools defence appealed in vain for offside.
Flinders then brilliantly denied Angelo Balanta and Luke Chadwick, while Dean Lewington curled a free-kick just wide and Shaun Williams had a headed goal ruled out for a shove.
Hartlepool rarely threatened in the first half but Jonathan Franks wasted a rare opportunity when he raced onto Jack Baldwin's long punt but could only lob straight at keeper David Martin.
Pools improved after the break and Charlie Wyke had a fierce drive beaten out by Martin and Steve Howard nodded a decent chance straight at the keeper.
But the Dons regained control and Chadwick had a low strike well saved by Flinders, while Potter drilled a shot narrowly wide and then blasted another effort against the crossbar at the death.