Dons skipper Mark Kerr had broken the deadlock after 26 minutes with his first goal since 2006 but Liam Kelly equalised with just over 20 minutes remaining.
The comeback was complete when Aberdeen transfer target Kevin Kyle powered a header beyond Stuart Nelson.
Jimmy Calderwood's side had gone into the match on a dire run of 10 defeats in 11 matches but will fancy their chances of staying up after securing three vital points.
Aberdeen made three changes to the side that slumped to a 3-1 home defeat against Hamilton for their Clydesdale Bank Premier League clash with Kilmarnock at Pittodrie.
Stuart Nelson replaced goalkeeper Jamie Langfield while striker Darren Mackie and midfielder Gary McDonald came in for suspended duo Richard Foster and Zander Diamond.
Kilmarnock, looking to avoid their 11th defeat in 12 matches as they teeter on the brink of relegation, made five changes to the side that lost 2-1 to St Johnstone.
Alan Combe replaced Cameron Bell in goal while Killie boss Jimmy Calderwood also handed starts to James Fowler, Manuel Pascali, Gavin Skelton and former Don Scott Severin.
Craig Bryson retained his place in the starting 11 despite suffering a broken nose at the weekend.
Kilmarnock had only scored four goals away from home prior to this match but they made a lively start with Aberdeen's central defensive paving of Jerel Ifil and Charlie Mulgrew called upon to make a couple of timely interventions.
An intelligent pass from Tim Clancy released Kyle after 11 minutes but the striker failed to find the target with his cute lob.
The Dons, already safe from relegation, struggled to penetrate the visitors' defence in the opening stages although Sone Aluko's low drive was blocked by Severin in a rare attack.
However, the home side broke the deadlock and from the most unlikely of sources.
Captain Kerr, who had been booed by his own supporters during the weekend defeat, was perfectly positioned on the edge of the Kilmarnock area to collect a loose ball from an Aluko corner and unleashed a powerful strike past the helpless Combe.
The home side were screaming for a penalty just before the break when Derek Young fell in the box under pressure from Severin but referee Crawford Allan waved play on.
Kilmarnock made a half-time switch with Danny Invincible replacing Skelton and the visitors almost grabbed an equaliser within six minutes of the restart but Stuart Nelson denied Frazer Wright with a smart save.
Pascali was then unfortunate to see his header come back off the post as the away team pushed for the leveller.
Killie should have restored parity after 61 minutes but Kyle somehow blasted over with the goal gaping after McDonald had cleared Bryson's low shot off the line.
The Ayrshire side were enjoying sustained period of pressure and finally got back on level terms after 69 minutes when Kelly's shot from the edge of the area beat Nelson courtesy of a deflection off Mulgrew.
And the visitors' comeback was complete after 74 minutes when substitute Graeme Owens crossed for the unmarked Kyle who powered the header past Nelson to the delight of the vocal travelling support.
Mark McGhee introduced promising youngster Clark Robertson for the tiring Young in the closing stages but the Dons could not force an equaliser and were forced to settle for back-to-back home defeats.