The Eredivisie side were kept at bay for an hour before Memphis Depay opened the scoring, and fellow teenager Jurgen Locadia then doubled the lead in the 75th minute.
Ligue 1 side Lyon were made to work hard for a 1-0 first-leg lead over Swiss outfit Grasshoppers, defender Milan Bisevac with the only goal midway through the second half.
Basle were 1-0 winners at home to Maccabi Tel Aviv, Valentin Stocker with the only goal six minutes before half-time.
Zenit St Petersburg were victorious by the same scoreline against Danish side Nordsjaelland, Russia striker Alexander Kerzhakov on the scoresheet four minutes after the interval.
Steaua Bucharest will be confident of progressing after a 2-0 win in their away leg against Dinamo Tbilisi, 19-year-old substitute Gabriel Iancu with both goals.
Dinamo Zagreb were made to wait until the 89th minute before Ante Rukavina scored the only goal of the game to give them a lead to take to Moldova for their second leg against Sheriff Tiraspol.
Marko Devic scored both goals, the first a penalty, in Metalist Kharkiv's 2-0 away win over PAOK Salonika, while Marian Cisovsky netted a hat-trick as Plzen won 4-0 away to Nomme Kalju.
In the night's other games, Austria Vienna won only 1-0 against Iceland's FH Hafnafjordur but Kazakhstan's Shakhter Karagandy took a commanding 3-0 lead against Skenderbeu of Albania.
No British sides were in action on Tuesday with Celtic due to face Swedish club Elfsborg on Wednesday.
The first English side to enter the competition will be Arsenal in the next round.