The 21-year-old defender was dismissed for an early reckless challenge on Steelmen winger Zaine Francis-Angol at Fir Park.
That left his Pittodrie colleagues up against it but they stunned Stuart McCall's men when Andrew Considine and Johnny Hayes each netted in the final 10 minutes to secure a surprise semi-final slot.
Fellow youth-team graduate Peter Pawlett was forced to fill in for his friend Shaughnessy at right-back but enjoyed his duel with Francis-Angol.
Pawlett, who is usually a midfielder, revealed manager Derek McInnes ensured the man he replaced learned a costly lesson following his first senior red card.
Pawlett told RedTV: "The reaction in the dressing room afterward the game was amazing. I think it is one of the best games I have been involved in.
"The journey up the road was good as well thanks to big Joe's treat. As his punishment, he had to buy all the boys a fish supper as a way of saying sorry to everyone, which was decent."
Pawlett may have to deputise for the suspended Shaughnessy once more on Monday night when Partick Thistle visit Pittodrie in the Scottish Premiership.
But the 22-year-old says he would have no qualms about dropping back into defence again.
"It was a new position for me in the second half but I really enjoyed it and I thought we were very good defensively," Pawlett said.
"In Francis-Angol I was up against a very good opponent and I think he has been their best player this season.
"The first time the ball went to him I said, 'Right, he is not getting past me here'.
"I managed to keep him goal-side and I grew in confidence from that moment on. I was pleased with my performance and I thought we dealt with him quite well.
"When Joe got sent off I did think, 'Oh no'.
"When we went down to 10 men we knew we had to get two banks of four with someone up top. We let them come onto us but all they could produce was shots from outside the box. Russell Anderson, Andy Considine and Mark Reynolds were unbelievable at the back. They won every single header.
"It was good for me to play alongside Russell. As it was a new position for me he really helped me through the game. It made it easier for me. Our support also helped me and all the boys through the game. There is no doubt they made a massive difference."