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.
Tensions are still high between the two countries after Nagorno-Karabakh clashes in 2013 occurred in mostly Armenian-controlled territories and saw many people killed.
They have been grouped with PAOK Salonika, Belarusian champions BATE Borisov and Hungarian title-winners Vidi.
Celtic are in something of a tough Group B, alongside Rosenborg, Salzburg and RB Leipzig. The club spent more than $200 million on players a year ago under new Chinese owners and failed to comply with UEFA rules monitoring transfer fees and wages.
Defending champions Atletico Madrid will not be participating in the group stage, as they secured qualification for the Champions League.
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.
Villarreal, Rapid Vienna and Spartak Moscow await in Group G as the Scottish side return to a European group stage for the first time since the 2010-11 Champions League.
The first round of matches will be played on Thursday, Sep 20.