Miroslav Stoch struck in the 73rd-minute strike in Gelsenkirchen after the hosts had gone 1-0 up just after the half-hour mark when Jefferson Farfan guided a shot in off the post.
The outcome was the same in Steaua Bucharest's home clash against Legia Warsaw.
Federico Piovaccari put Steaua ahead in the first half by hoisting a bouncing ball over advancing goalkeeper Dusan Kuciak, with Jakub Kosecki then making it 1-1 by sweeping in an equaliser after the break.
A 2-0 away win put Austria Vienna firmly in the driving seat of their tie against Dinamo Zagreb, Marin Leovac and Marko Stankovic providing the goals in the final 22 minutes of the contest. In between those strikes, Dinamo were reduced to 10 men, with Ante Rukavina being sent off.
Basel also look very much in control of their play-off having triumphed 4-2 at Ludogorets Razgrad.
The home side had come from behind to lead 2-1 thanks to goals from Marcelinho, who cancelled out Mohamed Salah's opener, and Ivan Stoyanov.
But Salah then brought things level once more and a Giovanni Sio finish and Fabian Schar penalty - awarded for a foul that earned Junior Caicara a red card - subsequently wrapped up the victory for the Swiss.