The Gunners could have found themselves behind at the interval if not for some poor finishing from the visitors, who were in action for the first time since the plane carrying club-record signing Emiliano Sala - as well as pilot David Ibbotson - went missing last week.
Daffodils were placed on the centre-circle before kickoff and Arsenal paid their own tribute by including Sala's name in Cardiff's squad on the back of the matchday programme.
Strike partner Alexandre Lacazette added a second late on and, while Nathaniel Mendez-Laing did manage to pull one back in stoppage time, Arsenal saw things through to make it back-to-back wins in the Premier League, taking them level on points with Chelsea in fourth place.
Cardiff had failed to beat Arsenal in their last 15 attempts and the early signs did not look too promising for the visitors, as Neil Etheridge could only tip a cross into the path of Lacazette, who should have done better than blast into the body of Manga on the line.
Arsenal failed to create another chance of note in the rest of the first half, though, with Cardiff looking the more threatening side.
Both sides were denied a penalty in the space of a few minutes, with Oumar Niasse being taken out by a mixture of Nacho Monreal and Sead Kolasinac, while Lacazette felt he was clipped by Manga - an incident that would repeat itself later in the half.
Arsenal struggled to get in behind Cardiff's compact defence and the Bluebirds enjoyed plenty of promising moments, but the away side could not make the most of their opportunities in a goalless first half.
Another decent chance came and went for Cardiff striker Niasse, whose shot was blocked in front of goal by Shkodran Mustafi, and the division's second-lowest scorers' profligacy would come back to haunt them.
Manga was this time penalised for clearly catching Kolasinac in the box and Aubameyang calmly slotted the ball past Etheridge to give Arsenal the lead.
Iwobi nearly doubled his side's tally by waltzing through and getting a poked effort on target, which Etheridge was equal to, but a second Arsenal goal would follow seven minutes from time thanks to Lacazette's clinical finish.
The Frenchman got away from Sol Bamba, drove into the box and fired the ball through Etheridge, giving Arsenal a two-goal advantage that would come in handy because of Cardiff's consolation.
Mendez-Laing steered the ball out of Bernd Leno's reach from a rare shot on target four minutes into added time, but it was not enough for City to earn a point on a night when the result was always going to be secondary in the wake of events off the field over the past week.
ARSENAL (4-3-1-2): Leno; Lichtsteiner (Jenkinson 60'), Mustafi, Monreal, Kolasinac; Elneny (Iwobi 46'), Guendouzi, Torreira; Ozil (Ramsey 76'); Lacazette, Aubameyang
CARDIFF CITY (4-1-4-1): Etheridge; Peltier, Manga, Bamba, Bennett; Gunnarsson; Paterson, Arter (Harris 81'), Ralls, Reid (Mendez-Laing 70'); Niasse (Zohore 73')