Midfielder Semedo was shown a straight red card by referee Chris Foy for an alleged two-footed tackle on Bolton's Jay Spearing in the 85th minute.
"You can tell by the reaction of the players and Jose is distraught because there is nothing wrong with the tackle," manager Dave Jones said after his side's 1-1 draw.
"We know his game inside out and it's not his nature to go out and hurt someone. He has one foot on the floor and we will appeal the decision.
"Hopefully, the referee will look at it again and reverse the decision."
If the club's appeal is unsuccessful Semedo will serve a three-game ban for serious foul play and will miss next weekend's clash at local rivals Barnsley followed by the home game against Reading on November 2 and the trip to Derby a week later.
Wednesday have yet to register their first win of the season after 11 games in the Sky Bet Championship.
But Jones added: "I'm proud of them all. We were magnificent, we completely dominated the game and had chances to win it.
"Everybody gave absolutely everything and we haven't got what we deserved."