Moments after Ben Foster's error handed Arsenal star Pierre-Emerick Aubameyang what proved the only goal at Vicarage Road on Monday, Watford captain Deeney was dismissed.
The striker caught Lucas Torreira with his elbow as he ran past the Arsenal midfielder, referee Craig Pawson showing the red card after consulting with his assistant.
Deeney's red card proved a key factor as Watford battled despite being down a man, with Craig Cathcart and Adam Masina both hitting the woodwork for the FA Cup finalists.
Should Deeney receive a standard three-match ban he would return in time to face Manchester City in May's showpiece at Wembley, but he risked a further punishment as he left the field.
Television footage appeared to show Deeney swearing at Emery as he headed down the tunnel, but the Arsenal head coach claimed not to have been aware of the content of the striker's volley.
"I didn't listen to him," Emery told a news conference after Arsenal moved up to fourth in the Premier League table. "He said something – it doesn't matter what - but I said to him I didn't see it.
"I didn't see the red card. I respect the decision from the referee. It's clear it helped us, the decision. Playing with one less player is more difficult.
"But our goal gives us the advantage in the result. We didn't do all we wanted to do. We can be happy with the result. To win here is very important.
"The three points is the most important but also we worked on being consistent in our structure, defending their long balls and set pieces."
1 - Arsenal have kept an away clean sheet in the Premier League for the first time this season, ending a 15-game wait for a shut out on the road in the competition, since a 1-0 victory against Huddersfield in Arsene Wenger’s final game in charge of the Gunners. Timely. #WATARS pic.twitter.com/4jSJTzMbzg— OptaJoe (@OptaJoe) April 15, 2019
Emery's fellow Spaniard Javi Gracia was adamant Deeney did not deserve to be sent off for his challenge on Uruguay international Torreira.
"I don't agree but I respect the referee's decision. It's maybe a yellow card," Gracia told reporters.
"He doesn't have to explain to me anything. I could see the play. I could see the contact with his arm but never his elbow. I don't understand that decision.
"I never saw an aggression in the movement. I don't understand why the referee took that decision."
Watford were arguably the better side despite Arsenal's man advantage but suffered their first home loss of 2019 in any competition.
"It's not fair to speak about the game only speaking about the result," Gracia added.
"We did many things well, from the beginning the game was difficult for us. We conceded an early goal and after that sending-off, playing with 10 players against Arsenal was very demanding for us.
"It was tough for us but we tried. My players deserved the recognition not just about the result. I'm really proud of all of them."