Nicolas Pepe had come off the bench to seemingly win the game for the Gunners with his strike four minutes from time, but the hosts could not hold on to their advantage as Tomas Holes headed in an equaliser to earn Slavia a 1-1 draw.
The first leg at the Emirates Stadium looked set to end in a goalless stalemate as Arsenal passed up a number of fine chances.
Xhaka played the ball forward to Aubameyang, who turned and played in Pepe, with the Ivory Coast forward bursting into the box and finishing coolly.
Slavia reacted well and levelled in stoppage time as Leno turned a Lukas Provod shot onto the post and behind.
Provod took the resulting corner, which flicked off the unsuspecting Pepe and allowed Holes to stoop and head in at the back post with the last meaningful touch of the night.