The Spaniard was handed the reins at Emirates Stadium over the summer after being chosen as the man to succeed Arsene Wenger.
There was still time for Aubameyang and Iwobi to pass up another two great chances as Arsenal ended the half on top.
Former Nigeria player, Victor Moses was on the bench throughout the game, but his side came out victorious.
Arsenal's season got off with a very disappointing start after their loss to previous champions Manchester City last Sunday after goals from Raheem Sterling and Bernardo Silva.
"We started shaky, I don't know, maybe we didn't know what to do, but we picked ourselves up and got going", Iwobi said.
It's high time Arsenal also inculcate the much vaunted "pressing" in their style of play.
"He needs to do (it) in each match, be demanding for us but defensive moments are for each and every player".
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Emery stuck with a tried and tested 4-2-3-1 formation against City but has hinted the system, as well as the personnel, could change until he finds the right formula.
Emery added: "It is clear the result is not good for us but the process is continuing".
Meanwhile, Gunners defender Shkodran Mustafi believes there is an "aura" around Emery and feels he can take the club forward.
The win makes it two defeats out of two for Emery, with the Arsenal defence needing major work, while Granit Xhaka continues to labour in midfield.
The 22-year-old scored a supeb goal that leveled up for the Gunners in the first half but a Marcos Alonso's stunner in the 81st minute ensured they suffered their second straight defeat in the 2018-19 campaign. I don't mind playing on the left if Laca is in the centre.
"The possibility to play Aubameyang and Lacazette is okay because we tried that in pre-season", Emery told reporters ahead of the keenly anticipated London derby against Chelsea at Stamford Bridge. So I think we have to work and we need to improve. We were unable to cover the lost balls and press like a team, so we were really in trouble, but I think the players were really very good because at 2-2 it was not easy with Arsenal.