Substitute Nicolas Pepe thought he had earned the Gunners a slender quarter-final first-leg advantage when he broke the deadlock in the 86th minute.
But Tomas Holes headed home in the dying moments of the game from close range to give Slavia Prague a precious away goal.
The second leg in Prague takes place next Thursday (20:00 BST) and Gunners boss Mikel Arteta, despite his side conceding so late, still believes they will progress to the semi-finals.
“The mindset has to be to go there and score goals and win the game because we have to score if we want to go through,” said the Spaniard.
“I totally believe that we can go there and win the match, if not I wouldn’t be sitting here.”Gunners have it all to do
Arteta stated he was in “shock” after his side’s tame 3-0 surrender to Liverpool last weekend, a performance which brought stinging criticism from both fans and pundits.
He reacted by making six changes – three of which were forced because of injuries – to his starting line-up, with captain Pierre-Emerick Aubameyang the most high-profile casualty.
“Well, I cannot talk with everybody individually every week,” Arteta replied when asked how Aubameyang reacted to being dropped.
“We try to be transparent and communicate with the players as transparent as possible, for them to understand the role of the game that they have. When he came on he showed the right attitude.”Aubameyang, who has 13 league and cup goals for his club this season but none since 6 March, cut a frustrated figure as he watched Willian, from a free-kick, clip the outside of the post before Alexandre Lacazette raced through, only to hit the bar.
Aubameyang was finally sent on after 78 minutes and made an impact as his pass allowed club-record £72m signing Pepe to race into the box and produce a composed finish past keeper Ondrej Kolar.
But Arsenal failed to see the game out and Holes’ back-post header means Arteta’s side have it all to do against the 2019-20 Czech champions in a week’s time.
Arsenal face big Prague test
With the Gunners lying 10th in the Premier League table, 10 points off a top four spot, winning the Europa League represents their most realistic chance of securing a Champions League spot next season.
They have not graced the Champions League stage since 2016-17 and they face a big test next week if they are to make it through to the semi-finals of Europe’s second-tier club knockout competition.
While this was an improvement on their previous outing, Arsenal rarely looked convincing against opponents who have beaten Leicester City and Rangers this season.
Rob Holding had a header tipped over the bar when the game was goalless, but at the other end Bernd Leno saved Jan Boril’s deflected shot while Lukas Provod hit the post before Holes got to a rebound inside the six-yard area to head his side level in the 93rd minute.