Rhys McCabe gave the Owls the lead on 20 minutes with a stunning volley and Jeremy Helan added a second in stoppage time with a fine, angled finish.
But it was Sutton's failure to award a penalty after Yann Kermorgant appeared to be fouled in the box towards the end of the first half which led to Powell being dismissed, though the Addicks boss was told it was not an 'official' red card.
Powell said: "There were a number of incidents that angered me during the first half and I went to the referee at half-time and asked him about a penalty we didn't get.
"There was a goal ruled-out for off-side which was actually on-side and there were also a number of fouls on my players.
"I was asking for consistency and fairness but I didn't swear at the referee or point at him. He sent me to the stand because he said it was for the image of the game. He said I'd left my technical area but it was half-time so what was I meant to do?
"I spoke to him at half-time in his room and he stood by his decision.
"I was asking in a fair and concise way but obviously he didn't see it like that. He said it was not a sending-off but I had to sit in the directors' box.
"We started off very well but we were chasing it after conceding a wonder goal. We've just got to move on now."