A big old scrap ensued between Dele Alli and a number of Arsenal players, even Spurs manager Maurcio Pochettino was forced to split things up between both sets of players as tempers flared.
Emery has gained plenty of admirers during his time at Arsenal so far, one of whom is United midfielder Juan Mata, who played under the Spaniard at Valencia and recently described him as a "special" coach.
Tottenham flipped the match on its head within the half with goals from Eric Dier and Harry Kane, Dier heading in from a Christian Eriksen free kick and Kane scoring from the spot after Son Heung-min was judged to have been brought down in the area.
Pierre-Emerick Aubameyang gave the Gunners a first-half lead with a penalty, but Spurs seized the advantage back with two goals within four minutes.
Unai Emery suggested Arsenal's contract negotiations with Aaron Ramsey remain "closed" despite being impressed with the midfielder's form and focus.
"When we conceded the third goal it was tough for us to come back mentally, to find the energy to go and try to be again in the game".
"In the end when we conceded the fourth and the sending off of Jan Vertonghen, the game was over".
"In the week we had trained playing with the three at the back as we had done in the previous game but for us it is not a problem".
"I think we talk a lot about how much we've progressed in terms of dealing with racism in our country, but we still have moments like this that disturb you and concern you".
"We spoke in the dressing room and we were having good minutes in the game".
Sunday's win lifted Arsenal above their north London rivals and into fourth place in the table, leaving them eight points behind leaders Manchester City.