Niasse was shown a controversial straight red card midway through the first half by referee Robert Madley for the striker's challenge on M'Baye Niang.
But the Tigers overcame their setback with fine second-half goals from Lazar Markovic and Sam Clucas.
Television replays showed Madley's decision was harsh and it appeared to have dealt Hull's bid to stay out of the Premier League relegation zone a huge blow.
"Of course, we will appeal," said Silva, whose side remain two points clear of third-bottom Swansea with four games to play.
"I don't want to talk too much (about it) because I respect the work of the referee, it's not easy.
"We all make mistakes. I make mistakes sometimes, the players, referees as well.
"My feelings during the match were it was a yellow card - if it was a yellow card - and everybody who has seen the replay said it wasn't a red card.
"One decision was not good to us. The referee gave us problems. We achieved the win, but it wasn't easy."
The Tigers have now won six of their last seven league games at home under Silva, taking 19 points from a possible 21, and the Portuguese was delighted with his side's performance.
"It's another really important three points from a tough game after fantastic work by our players," he said.
"We played 65 minutes with 10 players against a good team, a team comfortable in the table after achieving 40 points last week, and they have good players. It wasn't easy for us.
"That red card gave us problems. But our boys did fantastic work and it was a fantastic atmosphere in our stadium as well. We played together again."
Read the full article on eurosport.co.uk: Hull intend to appeal Niasse red card after overcoming odds to defeat Watford