Iwobi partnered Alexandre Lacazette and Henrikh Mkhitaryan - who replaced the absent Pierre-Emerick Aubameyang - in the Gunners' frontline.
The 22-year-old connected with Sead Kolasinac's cross in the 16th minute with a volley that was deflected by Terence Kongolo on its way to the net.
The Super Eagles forward took his tally to three goals in 23 league outings for Unai Emery's side this season.
Lacazette's tap-in from Ashley Maitland-Niles' cross on the stroke of half-time was enough for the Gunners to grab maximum points on the road despite Kolasinac's own goal in the stoppage time of the encounter.
The victory comes as a boost for their top-four ambitions after last Sunday's defeat to Manchester City as they climbed to fifth in the league log with three points above Chelsea who have a game at hand.