Borussia Monchengladbach, also hoping to qualify for the first time, have been paired with Ukraine's Dynamo Kiev, who have reached the semi-finals three times.
The first legs take place on August 21/22 with the returns a week later.
Italy's Udinese, beaten by Arsenal at the same stage last season, will face Braga of Portugal. Defeat would leave Italy with only two teams in the group stage.
Malaga finished fourth in La Liga last season but their outlook is uncertain after they announced "internal restructuring" amid reports that Qatari owner Sheikh Abdullah Bin Nassar Al-Thani wants to sell up after only two years.
In the last week, midfielder Santi Cazorla has joined Arsenal while Venezuela forward Salomon Rondon has moved to Russia's Rubin Kazan.
Their Greek opponents will be attempting to reach the group stage for the 10th time.
In other ties, Spartak Moscow will face Fenerbahce, who were excluded from the competition last season over a Turkish match-fixing scandal, and Lille will meet FC Copenhagen.
Cypriot champions AEL Limassol, hoping to emulate compatriots APOEL Nicosia who reached the quarter-finals last season, must first beat Belgian champions Anderlecht.
Celtic, the only former European champions among the teams in Friday's draw, were pitted against Swedish champions Helsingborg.
There is no English side in the play-offs because Chelsea won the Champions League last term and therefore go straight into the group stage despite having finished outside the Premier League's top four.
Draw:
Basel (Switzerland) v CFR Cluj (Romania)
Helsingborgs (Sweden) v Celtic (Scotland)
BATE Borisov (Belarus) v Hapoel Kiryat Shmona (Israel)
Limassol (Cyprus) v Anderlecht (Belgium)
Dinamo Zagreb (Croatia) v Maribor (Slovenia)
Braga (Portugal) v Udinese (Italy)
Spartak Moscow (Russia) v Fenerbahce (Turkey)
Malaga (Spain) v Panathinaikos (Greece)
Borussia Monchengladbach (Germany) v Dynamo Kiev (Ukraine)
Lille (France) v FC Copenhagen (Denmark)
