The Dons goalkeeper was shown a straight red card for hauling down Borja Perez, and Liam Kelly converted the resulting penalty.
Kelly's second made the game safe four minutes from time to the delight of Nicholl, who orchestrated things from the dugout with manager Kenny Shiels beginning a four-game touchline ban.
"It was a great run from Borja Perez and he kept on going. I thought he had over-run it. It's hard to say, and I've not seen the replay so I can't say whether it was a penalty or a red card or not. That was a wee break," Nicholl said.
"We weren't doing too badly. The way things have been recently, we wanted to keep it tight. It probably sounded negative to the players, but we were just hoping to come up here and have a decent performance, and hopefully take something from the game.
"The second half, Aberdeen certainly came at us and posed us problems. I was grateful to see the second goal go in.
"When you play against 10 men and are 1-0 up, you have an advantage. You should be confident and should be making the opposition work hard to get the ball off you.
"We didn't do that, and the players know they needed to do more with the ball.
"Personally, I was just delighted to get the points in the bag. The manager will be saying something different but, for me, it was all about getting three points away from home."