Olley: Baffling to see Aubameyang not play in a big match
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It looked as though substitute Nicolas Pepe's 86th-minute effort had given the hosts a narrow advantage to take to the Czech Republic for next week's second leg.
An often subdued game was punctuated by good chances for both sides with Arsenal guilty of wasteful finishing.
Slavia, who have beaten Leicester City and Rangers en route to the quarter-finals, had their moments too and substitute Petr Sevcik squandered a good chance to put them ahead while Lukas Provod had a shot turned against the woodwork seconds before Holes pounced to equalise.
It was a disappointing night for Arsenal whose season rests on going all the way in the Europa League.
Although they created plenty of chances, they looked fragile and lacked intensity until captain Pierre-Emerick Aubameyang, surprisingly left on the bench, and Pepe came on.
Arteta, who said he was shocked by his side's meek defeat by Liverpool at the weekend, looked aghast at the final whistle.
"The game was under control, we got the goal that we wanted, but then we played two or three balls in areas that we should not do and we put ourselves on the back foot," he said.
"Obviously [the late goal] changes the feeling."
The last time Slavia Prague visited Arsenal they lost 7-0 in a 2007 Champions League tie but they provided far more resistance this time.
Peter Olayinka had the first shot on target while Provod flashed a drive over the bar, although Arsenal should have gone in front when Saka was played in by Rob Holding but wastefully curled his shot wide of the post.
Saka was tripped just outside the area after outpacing the Slavia defence early in the second half and from the resulting free kick Willian found the outside of the upright.
After a period of Slavia possession Arsenal broke forward and Lacazette had the freedom of the pitch to run into, but with only keeper Ondrej Kolar to beat he hoisted his shot against the crossbar when it looked easier to score.
Lacazette scooped another chance over before Arteta sent on Pepe, Aubameyang and Mohamed Elneny in the 76th minute and it almost paid dividends but Aubameyang failed to finish from in front of goal.
Aubameyang played the pass that sent Pepe racing away and he outpaced the Czech defence before delicately clipping the ball beyond Kolar into the corner.
Arsenal celebrated hard but it was Slavia's players who were joyous at the full-time whistle after earning a precious draw for the Czech champions.
"It is superb to score a late equaliser against Arsenal, what else I can wish for?," Holes said. "I will remember it until the end of my life. We got a superb result."