The Aston Villa boss was quizzed on what happened after his side beat the Gunners 1-0 at Villa Park.
It was noted that Emery did not go over to the opposition bench amid the wild celebrations.
Quizzed on the apparent snub, Emery said: "No, because [Mikel] Arteta wasn't on the bench.
"I gave my hand to the workers inside because they were there when I was there, but only with the people I coached with and who worked with me.
"There was nothing personal. It was because it wasn't Arteta. I respect a lot Arsenal and Arteta. I respect a lot the workers there. I have nothing negative against them."
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Arteta had to watch the game from the stands after serving a touchline suspension, with his assistant Albert Stuivenberg delivering the messages to the team.
Villa have now won 15 Premier League games in a row and have beaten Man City and Arsenal in the space of a few days.
Emery stuck with the same starting XI and his decision ultimately paid off.
"They were excited and I was thinking at the beginning to do some changes to the starting XI because some were tired from Wednesday," he said.
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"It was a big effort, but we were speaking yesterday with the doctors and all of the players wanted to play today, they were all telling us they were perfect.
"During the match I was watching and needed to be clinical with my decision in changing players.
"Clearly I am very proud of our matches we play here. We have won 15 matches, I have never been in this situation.
"We have to enjoy it and still be demanding, we are achieving. The last time we lost here was against Arsenal and today we competed against them. We are increasing our demands and our level, being consistent, responsible and mature."