The Gunners had lost to Manchester City and Chelsea in Emery's first two games at the helm and could easily have slipped to a third defeat before eventually running out 3-1 winners at the Emirates Stadium.
It will be interesting to see whether Emery decides to play both Alexander Lacazette and Pierre-Emerick Aubameyang in a 4-3-3 formation or whether he will stick with the 4-2-3-1.
Arsenal introduced Alexandre Lacazette in place of Alex Iwobi at the break but it was Shkodran Mustafi who nearly put the hosts in front soon after the restart - Fabianski again making a smart stop to keep out the German's header.
Despite the win and the three points, Emery said there were still many things that could improve. "We need this control with possession with the ball and also going forward with balance, which is important".
Accentuating the positives of Arsenal's spirited comeback, Emery added: "We improved in the second half and controlled more like we want".
Felipe Anderson continued to probe, flashing agonisingly across the face of goal in injury-time, meaning Arsenal nerves only settled when Welbeck swivelled to dispatch Bellerin's pass.
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Details of the illness were not disclosed by the club as the former German worldwide sat out the Gunners third league game of the season.
Such was the case when Spaniard Unai Emery was chosen to be the man to usher in a new era at the Emirates, telling Wilshere that he was elcome to stay, but would not be in the starting line-up. Emery evidently is unafraid about clashing with the biggest personalities at Arsenal.