The Scottish side were taking on Slovenian side Maribor and needed to score after the first leg ended 1-1.
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Aberdeen also released a statement of condolence as news broke of the tragic deaths.
Aberdeen needed to score, after the first-leg finished 1-1, and were presented with the flawless opportunity after 25 minutes when they were rewarded a penalty.
Lewis missed and watched as the ball trickled right into the net.
Striker Adam Rooney had a first-half penalty saved, but advantage should have been played for the initial foul that saw the ref award the spot-kick because Niall McGinn had scored after the foul.
They came even closer with three minutes to go before the break when an Andrew Considine header allowed Graeme Shinnie to burst through, but Aberdeen were again denied by a splendid save by the keeper, who had raced from his goal to save with his feet again.
McInnes threw on Miles Storey in a desperate bid to get that goal and Aberdeen were still having the better of the encounter.
However, Popov’s decision to dismiss Stockley for two harsh yellow cards was a huge blow.
The Dons desperately pushed for a victor but it was the hosts who claimed victory when Shinnie’s attempted back pass bounced over the foot of keeper Joe Lewis and into his own net, sending Maribor into Friday’s draw for the final set of qualifiers with a 1-0 win.
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Aberdeen lost 1-0 on the night and 2-1 on aggregate.
