Diallo headed in Jude Stirling's long throw to break the Quakers' dogged resistance and rob Dave Penney's men of a fourth successive clean.
Milton Keynes dominated a subdued first half and Dean Lewington and Aaron Wilbraham both had 18-yard volleys deflected just wide before Ian Miller's superb last-ditch sliding tackle on Lloyd Dyer in the box denied the Dons winger in the 14th minute.
The sliding Wilbraham volleyed Dyer's deep cross into the side-netting from an acute angle in the 27th minute as the probing Dons struggled to create clear chances against the well-drilled Quakers defence.
The Dons upped the tempo after the break but Diallo's powerful 15-yard header flew straight into the grateful arms of Darlington goalkeeper David Stockdale from Lewington's outswinging corner six minutes after the re-start.
MK skipper Keith Andrews then skewed his right-foot shot wide from 22 yards before Leon Knight's goal-bound 10-yard curler was heroically blocked by the flying Miller.
At the other end, Quakers striker Pawel Abbott forced Dons keeper Willy Gueret into his first save of the afternoon in the 68th minute with a long-range daisy-cutter that he dived to gather easily.
Dons substitute Jemal Johnson sliced wide from the edge of the box after Stockdale had dropped Stirling's long throw before the Darlington keeper redeemed himself by acrobatically tipping over Lewington's rasping 18-yard drive.
Diallo headed another Stirling long throw inches wide in the 77th minute as the hosts' frustrations grew but Diallo went one better a minute from the end by glancing a 15-yard header inside the far post to snatch the points.