The midfielder's goal from a scissor-kick volley after 49 minutes was enough to separate the sides in a drab affair.
The Dons were worthy winners against a Kilmarnock side that offered little going forward.
However, the Ayrshire side could have stolen a point in the closing stages but Jamie Langfield rescued the Dons with two fine saves to thwart substitutes Mark Burchill and Kevin Kyle.
Aberdeen midfielder Gary McDonald returned to face his former club at the expense of Peter Pawlett who dropped to the bench.
There was also a place on the bench for defender Zander Diamond who has missed the vast majority of the season following an ankle injury and a broken nose.
Kilmarnock manager Jimmy Calderwood, who left Aberdeen in May last year, made four changes as he looked to get one over his former club with Danny Invincibile, Mehdi Taouil, Gavin Skelton and David Fernandez all handed starts.
Top scorer Kyle started on the bench with James Fowler, Frazer Wright and Conor Sammon also missing out.
Calderwood needed a police escort when he returned to Dunfermline as Aberdeen manager in 2004 but no such precautions were necessary today with the former Dons manager receiving a warm reception from the home support.
The game started in a scrappy manner with both sides struggling to create much in the final third.
The first real chance of the match fell for Killie's Craig Bryson who sent a powerful volley past the post after 22 minutes before Young shot wide from distance at the other end a minute later as the match finally came to life.
Aberdeen increased their tempo and Kilmarnock goalkeeper Cameron Bell was at full-stretch to turn a Darren Mackie drive round the post after 27 minutes.
Jerel Ifil was next to be denied for the Dons a minute later when the defender's header from a Paul Marshall corner was cleared off the line by Garry Hay.
Mackie was next to curse his luck when he failed to find the target with an acrobatic effort after Young had nodded a Richard Foster cross into his path after 34 minutes.
On the stroke of half-time Manuel Pascali was in the right place to block a McDonald shot to ensure his side went in goalless at the break.
Aberdeen made an explosive start to the second half when they took the lead in spectacular fashion after 49 minutes.
Simon Ford's weak clearance from a Davide Grassi throw-in fell for Young whose left-footed scissor-kick flew into the top corner giving Bell no chance.
The Dons pressed for a second to put the result beyond doubt with McDonald drawing another save from Bell with a low drive after 56 minutes. The midfielder went even closer three minutes later from a Fraser Fyvie corner which was headed off the line.
Kilmarnock made a double change after 64 minutes, introducing Kyle and Steven Old for the tiring Fernandez and Jamie Hamill.
Pascali prevented Mackie doubling the lead when the Italian managed to clear a menacing McDonald cross with the Dons striker lurking.
The Dons' support were appealing for a penalty in the closing stages when subtitute Pawlett tangled with Pascali in the box but referee Iain Brines waved play on.
Burchill, who had replaced the ineffective Allan Russell, almost equalised at the death but his well-struck volley was clawed away by Langfield.
And the points were made save for the home team when the Aberdeen stopper denied Kyle before Young rattled the crossbar on the full-time whistle.