A wasteful Arsenal conceded a stoppage-time equaliser to give Slavia Prague the advantage with an away goal following a 1-1 draw in their Europa League quarter-final first leg.
Defender Tomas Holes scored a header in the 94th minute, after Nicolas Pepe thought he had earned Mikel Arteta’s side a win with a goal off the bench late on.
The Ivory Coast international linked up with fellow substitute Pierre-Emerick Aubameyang, chipping a finish over the visiting goalkeeper Ondrej Kolar with four minutes of regular time remaining.
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Arsenal had been wasteful up until that point, with Bukayo Saka missing a one-on-one and Willian hitting the post, before Alexandre Lacazette passed up a huge chance, stealing the ball inside his own area and running the length of the pitch before scooping his shot on to the upright.
Slavia go into the second leg in the Czech capital just ahead in the tie, and will be looking to put another British side out after already beating Premier League side Leicester and Scottish Premiership champions Rangers.
Despite dominating the first-half, Arsenal struggled to impose themselves on the game and were slow in their build-up against a Slavia side well set up by boss Jindrich Trpisovsky.
'Not what we expected' - Arteta on Arsenal draw with Slavia Prague
Saka, making his return from injury, was by far the brightest player in the opening period and missed a huge chance when one-on-one with Kolar, with the England international cutting in from the right and putting his side-footed shot wide of the far post.
The north Londoners improved slightly for the final 10 minutes before the break and Rob Holding forced Kolar to tip the ball over the bar after getting on the end of a Cedric Soares cross on the left, but they were the only real chances for either team before the interval.
Arsenal started the half well and Saka picked up from where he left off, winning a free-kick on the edge of the area early on, which Willian clipped the post with from a difficult angle.
But the biggest chance came when Lacazette did well to win the ball off Oscar Dorley inside his own half, before running the length of the field. With only Kolar to beat, the French striker looped his effort on to the upright.
Arteta’s men had improved but were slow in the build-up, and it was only the introduction of Aubameyang and Pepe late in the game which sparked them into life.
Aubameyang almost made an instant impact from a Pepe cross, until they switched roles, with the Ivorian producing a lovely finish over Kolar to give the home team what they were sure was a winning goal.
But Slavia had one more opportunity to attack and Lukas Provod forced a save at the near post from Bernd Leno right in stoppage time to earn a corner.
Arsenal switched off from the resulting set-piece, the corner coming off the back of Pepe and diverting to Holes, who stooped low to put a header past the German goalkeeper.
The result puts Slavia just ahead of the tie with their away goal ahead of the second leg in Prague next Thursday (April 15).
TALKING POINT - ARTETA TOO LATE TO MAKE CHANGES?
Arsenal were wasteful with their chances and slow in their build-up play. It was crying out for the big names to come off the bench, but Pepe and Aubameyang did not enter the field until the 78th minute.
Their impact was instant, and had they not conceded late on it may have looked like a masterstroke from Arteta.
But once again, Arsenal switched off at the back and the result leaves them with much to do in the second leg.
MAN OF THE MATCH - BUKAYO SAKA
Although he missed a great chance in the first half, the England international was the only Arsenal player who really looked like creating something for much of the game.
All of the home side’s best opportunities came through him, before he was brought off for goalscorer Pepe.
Giving man of the match to a substitute who played 15 minutes would be a stretch, but Pepe’s impact was huge, too.
ARSENAL: Leno 6, Bellerin 6, Holding 6, Gabriel 6, Cedric 6, Partey 6, Xhaka 6, Saka 8, Smith Rowe 6, Willian 6, Lacazette 5...Subs: Elneny 5, Ceballos N/A, Pepe 8, Martinelli 6, Aubameyang 7.
SLAVIA: Kolar 7, Bah 6, Holes 7, Zima 6, Boril 6, Hromada 6, Oscar 6, Stanciu 6, Provod 7, Olayinka 6, Sima 6…Subs: Kuchta 6, Sevcik 5, Masopust N/A, Lingr N/A, Traore N/A.
94+4’ - GOOOOOAL! Disaster for Arsenal. A corner from the right comes off Pepe and finds Holes, who puts a bullet header into the back of the net! Slavia have the away goal.
86’ - GOOOOAL! It's Pepe! He's looked great since coming on and the forward breaks through from an Aubameyang ball, with his left foot he dinks his effort over the goalkeeper and Arsenal lead. The subs have made the difference!
82’ - CHANCE! good chance falls to Martinelli just inside the box, his effort is tipped over the bar by Kolar.
78’ - ALMOST AN INSTANT IMPACT! Smith Rowe links up well with Pepe and then puts a lovely cross in from the right, but Aubameyang can't get a decent enough connection on it and his effort goes wide.
77’ - MASSIVE CHANCE FOR SLAVIA! Cedric's clearance from a cross is poor and it's only as far as Sevcik, who shoots wide inside the box.
62’ - HUGE CHANCE! How on earth has Lacazette not scored this?! He steals the ball on the half-way line and runs the length of the half with no one in front of him. The French striker takes his time to pick his spot - but hits the upright. Massive opportunity missed for the home side.
58’ - CHANCE! Best opportunity of the game for the visitors who work the ball well to Boril, but the captain's shot is saved by the legs of Leno.
49’ - OFF THE WOODWORK! Willian eventually takes the resulting free-kick, after a check to see if should actually be a penalty, and the Brazilian clips the post with a brilliant effort from the right edge of the box.
39’ - CHANCE! Arsenal keep the ball alive though and Cedric does use his left foot to get a decent cross in, Holding's still up from the free-kick and forces Kolar to tip his header over the bar.
29’ - CHANCE! Big chance for Saka, who beats the offside trap and drives into the box from the right. One-on-one with Kolar, he side foots his effort wide of the far post. The assistant referee raises his flag but replays show he was definitely onside. Best opportunity of the game and Saka should really score that.
Arsenal have now gone four games without a win in all competitions, and although their record of never losing to a Czech side remains intact, they are now at serious risk of that slipping.
This draw extended Slavia’s unbeaten run to an astonishing 21 matches, given they have also played teams like Rangers and Leicester in that time.
Nicolas Pepe’s goal was his fourth in the Europa League this season, more than any other Arsenal player.
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