The Gunners have been paired with Azerbaijani side Qarabag, Portuguese outfit Sporting Lisbon and Ukrainian side Vorskla in group E of the competition.
There has been a long-standing conflict between Armenia and Azerbaijan over the disputed Nagorno-Karabakh territory, and in 2016 at least 200 people were killed in clashes between the two nations.
Back in 2015 when Mkhitaryan was with Borussia Dortmund, he had to again stay back in Germany for a Europa League tie against Gabala, another Azerbaijan side, because of security concerns.
'We've talked to the player again, and it's the best decision for all involved.
Forty-eight clubs have been split equally into four pots, and the draw will see 12 groups formed containing one team from each pot, with teams from the same association being kept apart.
Celtic themselves also eased through a decade on from both Glasgow clubs competing on the Champions League stage - in their case with something to spare as they saw off Lithuania's Suduva 3-0 at home.
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Dudelange, the first club from Luxembourg to reach the group stage of the competition, were handed a trip to the San Siro to play AC Milan.
Rosenborg complete Group B and are a side Celtic know well having beat the Norwegian champions in a Champions League qualifier this summer.
Rangers, managed by former Champions League victor Sveven Gerrard, enjoyed better fortunes among the British contingent when they advanced 2-1 on aggregate after holding Russian side FC Ufa to a 1-1 away draw despite ending the contest with nine men.
Steven Gerrard's Rangers are also facing a hard group stage, having been pitted against Villarreal, Rapid Vienna and Spartak Moscow in Group G.
The first group games will played on September 20.