Fleetwood's thunderbolt and strikes from Alan Connell and substitute Rob Purdie ended the Bulls' four-match losing streak on the road, while Izale McLeod replied for the Dons, who had manager Martin Allen sent off.
Hereford started brightly and Fleetwood was denied by a good double save from Dons goalkeeper Adolfo Baines before Connell put the Bulls ahead in the eighth minute from close range.
The lively Fleetwood rode Dons' full-back Dean Lewington's poor challenge and was denied one-on-one by Baines, but Connell rammed the rebound underneath the floored stopper.
The lacklustre Dons tried to muster a response but Lloyd Dyer fired an angled drive straight at Hereford keeper Wayne Brown when well placed, before Bulls' substitute Purdie's 22nd minute spot-kick put the visitors' two-up.
Purdie crisply tucked his seventh goal of the season low into the corner with his first touch of the ball, after Dons' keeper Baines had needlessly pole-axed Andy Williams in the box when defender Ben Chorley appeared to have the situation under control.
The Dons were finally sparked into life and McLeod's left-foot volley was saved well by Brown, before Chorley's header from Jon-Paul McGovern's corner was hacked off the line by Bulls' skipper Tamika Mkandawire in the 34th minute.
McGovern blasted a 25-yard strike just wide, before Baines failed to gather a routine ball in the box at the other end but Fleetwood failed to capitalise as he fired badly into the side netting in the 41st minute.
The sluggish Dons laboured against a stubborn Bulls' back five in the early stages of the second half but a moment of inspiration from McLeod made it 2-1 in the 59th minute.
McLeod wriggled free of Hereford centre-half Phil Gulliver in the box and fired his eighth goal of the season low across Brown into the corner of the net from eight yards.
McGovern's deflected strike from edge of box was saved well by Brown as Milton Keynes pressed for an equaliser, before angry Dons manager Allen was sent to the stands by referee Darren Deadman for protesting too vehemently in the 65th minute.
Keith Andrews' rasping 25-yard drive was well saved well by Bulls' keeper Brown in the 67th minute, before Connell's cheeky 40-yard lob almost caught out Baines at the other end but it dropped inches over the bar.
Drissa Diallo's powerful header from McGovern's corner was cleared off the line by Bulls' midfielder Purdie in the 73rd minute, before Andy Williams' angled drive was well saved by Baines at the other end.
Andrews lashed Dyer's cut back wildly over the bar from 15 yards three minutes from the end, before Fleetwood made it 3-1 on the break when he lashed in from 18 yards at the death.