Eighteen-year-old Emile Smith Rowe, a product of the club's academy was on target as the Gunners maintained their winning start in the competition.
Sokratis Papastathopoulos and Matteo Guendouzi also scored for Unai Emery's side who sit atop Group E with six points.
Milan trailed to a Miguel Angel Guerrero goal at the San Siro but a late flurry of goals ensured victory for Gennaro Gattuso's side.
Patrick Cutrone scored twice for the Italians and Argentine Gonzalo Higuain was also on target as Group F side Milan also made it two wins out of two.
RB Salzburg came back from a goal down to beat Scotland's Celtic 3-1 in Austria.
Odsonne Edouard's cool finish put Celtic in front in the second minute but Munas Dabbur and Takumi Minamino scored after the break. Celtic's James Forrest was sent off after a foul in the area and Dabbur slotted home the resulting penalty to put the game beyond Brendan Rodgers' side
Substitute Lucas Alario scored a brace for Bayer Leverkusen in their 4-2 win over Cypriot side AEK Larnaca.
An emotional Alvaro Morata snapped his recent goal drought to secure a 1-0 win for Chelsea over Hungarian champions Vidi in the Europa League on Thursday (Oct 4), as Arsenal cruised to a 3-0 victory away to Qarabag in Azerbaijan.
Last year's runners-up Marseille threw away a two-goal lead in Cyprus and were forced to settle for a 2-2 draw against Apollon Limassol. Goals by Dimitri Payet and Luiz Gustavo put the French club in control, but Sasa Markovic pulled one back before Emilio Zelaya fired home in stoppage time.
Five-time winners Sevilla suffered a 2-1 defeat at Krasnodar as Tornike Okriashvili hit an 88th-minute winner for the Russians, while Eintracht Frankfurt beat nine-man Lazio 4-1.
