Just 48 seconds after the opening whistle, it was clear Emery's first win against the Spaniard would have to wait another day.
Manchester City striker Sergio Aguero continued his assault against Arsenal, scoring a hat trick to lift his career goal tally to 11 against the north London side.
The opener arrived courtesy of sloppy Arsenal defending, allowing Aymeric Laporte to feed a diving Aguero within the first minute of play.
Arsenal retaliated with a clever header from Laurent Koscielny off a set piece in the 11th minute -- the first time City conceded that early in a Premier League match in over a year, according to data providers Opta.
Aguero came back, however, scoring an easy tip-in off an assist from Raheem Sterling just before halftime. He was lucky to be awarded a third goal in the 60th minute, as replays showed the ball deflecting off the Argentine's left arm before inching over the goal line to seal the final score at 3-1.
Denis Suarez, the former Manchester City academy player on loan from Barcelona, made his Arsenal debut against his old team as a second-half substitute, but had little impact. Mesut Ozil once again did not get on the pitch for Arsenal, with the German's future at the club surely in doubt.
Defending league champions City bounced back from a shocking loss at Newcastle on Tuesday. They sit just two points behind leaders Liverpool, who play Monday night at West Ham.
"The important thing is that we realize what we have to do to win games," Guardiola said to Sky Sports after the match. "We are a good team when we go ... the full 90 minutes. When we are not in that rhythm and we go a bit slower, we are not a good team."
Arsenal drop to sixth place, one point behind Manchester United in a tight battle for top European play next season.
United on a roll
Earlier on Sunday Manchester United narrowly defeated Leicester City 1-0 at King Power Stadium behind a ninth-minute goal from Marcus Rashford.
The 21-year-old was making his 100th Premier League appearance for the club, and scored off an assist from Paul Pogba.
"Time and time again he provides opportunities for the team, that's what we want from him. If we can get him free as much as we can, then he can make these passes all day long," Rashford said of Pogba, who appears rejuvenated since parting ways with former United manager Jose Mourinho.