The advantage is with PAOK Thessaloniki in their Champions League play-off with Schalke following a 1-1 draw in Gelsenkirchen on Wednesday night.
The Germans had gone 1-0 up just after the half-hour mark when Jefferson Farfan guided a shot in off the post.
But the Greek side will head into the second leg on home soil in the box seat after Miroslav Stoch's 73rd-minute strike restored parity and also earned them a crucial away goal.
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.
Basle 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 Basle.
Arsenal's place in the group stage looks all but assured after they secured a 3-0 away victory against Fenerbahce.
The Gunners claimed their first goal six minutes into the second half when Kieran Gibbs turned the ball in from Theo Walcott's low cross.
Thirteen minutes later Aaron Ramsey added another, drilling an effort from outside the box that goalkeeper Volkan Demirel made a hash of trying to keep out.
Walcott was then bundled over in the area by Michal Kadlec and Olivier Giroud converted the resulting penalty on 77 minutes.