Goals in either half from Raheem Sterling and Bernardo Silva were enough to see Pep Guardiola's team emerge victorious in North London.
City beat the press
Emery deployed a 4-3-3 system with Aaron Ramsey the most advanced midfielder. Sitting behind him were Granit Xhaka and 19-year-old surprise starter Matteo Guendouzi.
Arsenal were clearly instructed to press City, this was evident from the first minute as Ramsey ran beyond striker Pierre-Emerick Aubameyang to try and close down City's centre-backs. Guendouzi, who had impressed in pre-season, saw a lot of the ball and was tasked with limiting the influence of midfield creator Silva.
However, the 19-year-old Frenchman had to shoulder some of the blame for the opening goal of the match. Sterling cut inside from the left channel and unleashed a shot beyond an unsighted Petr Cech who could only watch as the Gunners went a goal down. Guendouzi was late closing Sterling down and as a result, the England international had adequate time and space to have a shot on goal.
Hector Bellerin, who himself wasn't without blame for City's first goal, registered Arsenal's first shot on target, nutmegging Benjamin Mendy before seeing his lowly struck effort saved by Brazilian 'keeper Ederson.
This was as good as it got for the hosts in the first half, as they went in at half-time a goal down.
Arsenal huff and puff to no avail
Arsenal started the second half on the front foot. Maintaining possession in City's half for long spells without really creating any clear cut chances.
The visitors visibly dropped off to protect their lead and despite Arsenal growing into the game, Ederson remained untested. At the other end it was an almost a nightmare moment for Guendouzi, who's missed interception lead to Sergio Aguero being clear through one on one, however his tame strike was well saved by Cech.
But just one minute later City doubled their lead. Mendy raced through on the left flank and his well-timed cut back was beautifully dispatched by Silva into the roof of the Arsenal net. The Gunners were left with a very steep mountain to climb.
The introduction of Alexandre Lacazette and debutant Lucas Torreira injected a bit more urgency into Arsenal's game. Lacazette was on the field for mere minutes before his right-footed half-volley dropped just wide of Ederson's far post.
Minutes later Mesut Ozil was presented with a glorious chance to get his side back into the game. After Ederson's miss-kick, the ball fell to the German whose heavy touch saw the ball fall thankfully back into Ederson's grasp.
Arsenal continued to pour men forward but were unable to break down a determined City defence as they were beaten at home on the opening day of the season.
Emery's acid test
In Emery's defence, a first league game against the best team in the country is hardly ideal. But knowing the Spaniard's desire to win, he will have been disappointed that his new side unable to at least score against the reigning champions.
There were a few noticeable differences in Arsenal's style of play, one being the aforementioned pressing and another being the insistence on playing out from the back. Goalkeeper Cech had more touches against City than he had in any game under previous boss Arsene Wenger, something the former Czech Republic international must get used to.
One positive for Emery would've been the performances of Shkodran Mustafi and summer addition Sokratis. With doubts over the two centre-backs' ability to play with each other, the pair were barely exposed and had minimal - if any - part to play in the two goals Arsenal conceded.
Next up for Arsenal are FA Cup holders Chelsea, who are also adjusting to life under a new manager.
Will it be two defeats from two for Emery? Or will Arsenal quickly banish the memory of an opening day defeat with a commendable result at Stamford Bridge?