Aberdeen started very brightly and Accies keeper May saved well with his feet to deny Ryan Duncan in the fifth minute. Great persistence from Adam Emslie wide on the left saw him wriggle clear before delivering a cross which just eluded striker Liam Harvey as the Dons pushed for an opener their build up play deserved.
On the quarter hour Ethan Duncalf sent Alfie Bavidge racing forward and the in-form striker was once again denied by the outstretched foot of keeper Cammy May.
Aberdeen were well on top at this stage but then on 19 minutes disaster for the Dons.
A long clearance saw Meikle get on the wrong side of Timi Fatona and the defender's effort to get to the ball was penalised by referee Nicolson who saw the challenge as denying a goal-scoring opportunity and showed a straight red to the full back. It looked a very close call.
Just to make matters worse, Meikle took the free-kick from twenty yards and rifled the ball high into the net to give the visitors the lead, totally against the run of play.
Finn Yeats moved to full back with Adam Emslie swapping wings with Ryan Duncan as the Dons rejigged their formation. Emslie was unlucky not to win a penalty when he was fouled inside the area after a late tackle.
Accies then enjoyed the bulk of possession and forced a series of corners, Forsyth's inswinging deliveries from the right causing no end of problems for the Dons defence.
Just as it looked as though the first half would draw to an end with Accies a goal to the good, Meikle again fired in a fine shot which Oluyemi dived to his left to parry, but Gaffney was alert to the loose ball and slotted it into the net to make it 2-0 and give the home side a real uphill struggle.
The red card for Fatona was the turning point of a first half which the Dons had dominated until the full back's dismissal, but Accies will have been delighted to have taken advantage of their numerical superiority to go in at the break in a strong position.
Half time - Aberdeen 0 Hamilton Academical 2
Aberdeen were on the front foot from the whistle and created a number of good chances as the half wore on.
At the start of the second half Barry Robson was yellow carded after disputing a decision, referee Nicolson booked three home players in quick succession, Bavidge, Towler and McKenzie all falling foul of the official.
On 66 minutes a Bavidge cross from the right was fired over the top by Harvey as the Dons defied the odds by being dominant despite being a man down. Bavidge then saw a header knocked off the line by Meechan before heading wide as the pressure built on the visitors defence.
But any hopes of a comeback appeared to have gone when on 72 minutes, another red card for Aberdeen, this time skipper Evan Towler picking up a second yellow for a tug on the shirt of Meechan.
Despite now playing with nine, Aberdeen's fitness shone through and they continued to press, Bavidge skying a good chance after McKenzie knocked down a Dylan Lobban free kick.
On 90 minutes the Dons got the goal they craved as substitute Taylor Mason made a good interception and raced forward before delivering the perfect cross for Bavidge to bullet into the net, the striker's third goal in two games.
The nine men had a lifeline and the question was whether the visitors could hold out. And it looked as though the Dons might have got their just rewards when Emslie connected with a fine Duncalf cross but May held on at the second attempt to seal victory for his side. A very fine save.
So, another loss for the young Dons but the spirit and fitness levels were there in abundance and it is surely just a matter of time before their fortunes turn for the better. Next up as a Youth Cup last sixteen tie in Paisley next Friday against St Mirren.
Full time - Aberdeen 1 Hamilton Academical 2
Barry Robson: "I am extremely pleased with the fitness and how the boys were in the game tonight. We should still be coming away winning that game.
You could see their power and fitness.
"Even with nine men we looked good. We manage to score and almost forced an equaliser.
"I said to the players afterwards, that the worst thing in football is individual errors at the back and not taking your chances. That is what has cost us tonight, and has cost us in recent games. But they are young players and that is why we as coaches are here, to rectify that.
"There were a few decisions that I felt did not go our way but that happens.
"You learn a lot about your players in games like tonight. The boys showed a lot of character, it is just as I say the mistakes that our letting us down.
"Because most of the boys are playing up at least one level, that is why we are losing a few games at the moment, but we have a Youth Cup game to look forward to next Friday away to St Mirren."