The Dons lined up with Tomas Cerny in goal behind a back four of Ryan Harrington, Greg Halford, Michael Devlin and Jack Mackenzie. Miko Virtanen, Morgan Brown and Stephen Gleeson were in the engine room with Ethan Ross supporting Stevie May and James Wilson up front.
May was first to threaten for Aberdeen latching on to a nice ball forward from Devlin, his angled drive slipping just wide. Wilson had started the game in lively fashion and tested the keeper from the angle of the box as the home side pressed forward.
A neat move from the visitors ended with Scott firing the ball into the net on 10 minutes, but the flag was up for offside. It was the first occasion on which Dundee had ventured into the Aberdeen half.
Good work on the right from Harrington saw the full back create space for a cross, the delivery just too strong for the men in the box. The pace of May was causing the Dundee defence problems and they breathed a sigh of relief when a forward ball from Halford aimed at the hitman was just half a yard too strong.
On 19 minutes, Brown drew a fine diving save from Dundee keeper Jackson as his curling twenty-yard effort looked destined for the net.
Cerny was called into action on 24 minutes saving well at his near post from a deflected header as the visitors came more into the game. The match was being played at a quick tempo although chances were at a premium.
Jackson saved at the second attempt as Wilson fired in a dipping, long-range effort then Ross lobbed over when he will feel he should have been hitting the target. Despite the greater experience in the home ranks, the Dons were finding the Dark Blues difficult to break down.
A lovely chipped ball from Gleeson sent May racing in on goal, but Jackson was off his line quickly to save well. At the other end, Cerny saved brilliantly from Henvey after the ball had broken fortuitously for the Dundee striker.
It had been a lively opening period but neither side had anything to show for their efforts.
Half time - Aberdeen Reserves 0 Dundee Reserves 0
Both sides had early chances after the break, Brown forcing a save from Jackson before Scott was denied by a combination of Cerny and Mackenzie.
Henvey's stabbed shot following a free-kick was saved well by Cerny before May volleyed wide after Ross had fashioned a cross from a seemingly lost cause.
The deadlock was broken on 54 minutes when James Wilson hung up a delightful cross for Miko Virtanen to head back across the keeper into the corner of the net. Real quality from Wilson to create the chance and a fine finish from Virtanen to notch his second goal of the season.
An outstanding double save from Jackson denied first Virtanen then Wilson as the Dons piled forward but Dundee were always dangerous on the break and Scott should have done better than sclaff a shot wide on the hour mark.
Rice's goal-line clearance denied May then Jackson did well to block the striker after he'd been played in by the impressive Virtanen.
Cunningham replaced Mulligan in the Dundee side on 63 minutes as they attempted to stem the flood of red shirts towards their goal.
Lambert had a chance from a twenty-five yard free-kick for Dundee, but the defensive wall stood firm to block his curling effort.
Lloyd Robertson took the place of Harrington as Paul Sheerin made his first switch on 71 minutes, Dundee bringing Smith on for the hard-working Henvey a couple of minutes later. A second Dons substitution saw Mykyta replace Brown with quarter of an hour left.
Greg Halford, playing for the first time since December, was booked on 78 minutes after disputing a decision. Seconds later, May was within a whisker of making it 2-0, but his snapshot crashed off the keeper's left-hand post and away to safety.
Going into the final ten minutes, Aberdeen looked comfortable in the lead, but it was a slender advantage and Dundee were still showing ambition when they were in the Dons half, so concentration was required to see the game to a successful conclusion.
On 84 minutes, Lewis Duncan came on to replace Ross who had given his usual all-action display for Aberdeen.
Johnston took the place of Scott for the final couple of minutes but despite their best efforts they were destined to return south empty-handed as Stevie May finally got the goal he deserved, racing through to hammer the ball past a helpless Jackson to seal the victory.
A solid victory for an experienced Aberdeen side who were made to work hard by a Dundee side who battled until the end.