The home side had been in free-scoring form in their opening three competitive fixtures, racking up no fewer than eighteen goals without reply and were expected to be a major threat to the Dons youngsters' hopes of progressing in the tournament.
Sam Jackson was in goal behind a back four of Calvin Ramsay, Luc Bollan, Luke Turner and Lloyd Robertson. Miko Virtanen and Seb Ross were in central midfield flanked by Ethan Ross and Chris Antoniazzi. David Dangana and Michael Ruth were up front.
Both sides had early efforts on goal but neither keeper was forced into a save as first Williamson then Dangana tried their luck. A neat move featuring Seb Ross and Antoniazzi saw the skipper fire a dangerous ball across the face of the Brora goal but there was nobody in a gold shirt to profit.
The home side took the lead on 11 minutes when Nicolson fired the ball just inside Jackson's left hand post from 18 yards after he was found in space following a corner.
A fine run by Brindle saw him fire a cross into the six yard box, but the Dons defence scrambled the ball clear.
Jackson saved well from Davidson as Brora pushed for a second goal, the young Dons finding it difficult to create much going forward. Great work by Ethan Ross saw the winger trick a couple of payers as he drove into the area, the home defence doing well to block the cross at the expense of a fruitless corner.
Aberdeen came close to an equaliser on the half hour as Dangana picked out Seb Ross with a clever reverse ball. Unfortunately, the midfielder's left footed volley was just too high.
The home side were causing problems at set pieces and it took a desperate block to deny Gillespie. Luke Turner headed over after an Ethan Ross corner but as the clock ticked on to 35 minutes Brora keeper Malin had still to make a save of note.
Jackson saved well from Davidson after the front man was picked out by MacRae's cross, Brora playing a very attractive brand of football and showing why they are favourites to win this season's Highland title.
Malin was finally called into action two minutes before the break and produced a brilliant save to deny Antoniazzi after the Aberdeen man had been picked out in the area by Ethan Ross.
Brora had probably just about edged the first period playing some bright, attacking football and the Pittodrie youngsters had it all to do to get back on terms although there were promising moments in front of the home goal just before the break.
Half time - Brora Rangers 1 Aberdeen Under 21s 0
A controversial start to the second half saw the Dons have a strong penalty appeal waved away by referee Bruce after Ethan Ross had been tumbled in the box. Brora broke to the other end and Wagenaar crossed for Davidson to divert the ball past Jackson to make it 2-0. The kids had it all to do now.
Neil Macdonald was booked on 49 minutes after a foul on Ethan Ross, but the free kick couldn't pick out Turner at the back post. Brindle joined his team-mate in the book for another foul on Ethan whose trickery was causing Brora problems.
There were more loud claims from the Dons for a spot-kick after Seb Ross was bundled over, but again referee Bruce was unmoved as heavy rain battered down on the Dudgeon Park crowd.
Ethan Ross was replaced by Kevin Hanratty just past the hour, shortly before Ally MacDonald galloped forward for Brora before shooting wildly over with Davidson screaming for a pass.
On 65 minutes it was 3-0 to Brora, Norwegian winger Wagenaar firing a swerving 30 yard screamer past Jackson. Dangana came off to be replaced by Shanks.
Tempers were becoming frayed and Davidson was booked along with Virtanen after a clash in the Dons area. Things went from bad to worse for the Dons on 71 minutes as Dale Gillespie smashed a long range effort past a despairing Jackson to make it 4-0 to the Highlanders. Seb Ross then picked up a yellow for a clumsy challenge.
Just after Chesser had come on for Antoniazzi, sub MacLeod with his first touch completed a nap hand for the rampant Cattachs who were running riot.
Calvin Ramsay fired just wide from a free-kick as the Dons tried to at least get some kind of consolation from this bruising experience. Wagenaar was the next man cautioned for a late challenge on Hanratty after the Dons man had made a good break from midfield.
Williamson made it 6 of the best for Brora as he turned in a left wing corner to complete a miserable evening for the Pittodrie kids.
Brora showed some real class as they dominated the second half and ran out worthy winners.
Full time - Brora Rangers 6 Aberdeen 0
"Disappointed with the goal that we lose. We thought we could have dealt with that better. Going forward we thought we could have offered more in terms of runs beyond. It was a bit too comfortable for Brora, and when they got in their shape they made it difficult for us. We never overly tested them apart from Chris' chance from Ethan's good play.
"Ethan was the one real threat I thought throughout. He looked positive. He looked bubbly. He looked like the one who was going to create something for us.
"Then we lose the second goal and we are back to what have had previously. There was a 12 minute spell when we lose three goals. I am trying to get a hold of them and trying to get them to see the game out without losing any more goals, and before you know it you have lost an other one and another one.
"A recurring theme, and a worrying one.
"You use these experiences as a learning tool and when you are having recurring issues then you are not learning and that is a concern for us.
"Again, we need to take our medicine and we need to try and learn more than what we are doing at the moment.
"We had a strong penalty shout at the start of the second half and then they go up the park and score their second goal. I am not making excuses because they still travel 80 yards and we were a bit weak in the tackle. We have to be stronger. There was a lot that went on after the penalty. So yes disappointed because I thought it was a penalty, but we still have to defend better than that.
"We wish Brora all the best in the competition.
"We knew it was going to be difficult here. We knew how tough it would be to come away with something although I don't expect a 6-0 defeat.
"We did our homework, we knew what they were all about. We knew they had scored 18 goals in three games and kept clean sheets. So we knew it was going to be difficult but we thought we had done enough to prepare our players and to be a bit more competitive than we were in that second half."