Mehmet Topal netted the only goal of the game in the 36th minute with a 30-yard screamer that gave Asmir Begovic absolutely no chance.
Sofiane Feghouli also hit the post in the second half while Stoke, who have lost their past four Barclays Premier League games, were limited to half chances.
Two quick goals ensured PSV Eindhoven claimed an away win to give them control of their tie with Trabzonspor.
Tim Matavz and Ola Toivonen stunned the home side with strikes inside the first 12 minutes.
Trabzonspor pulled a goal back through Olcan Adin on the half-hour and, while they controlled possession for long periods, their horror start proved costly as they failed to find a leveller.
FC Twente claimed a vital away victory thanks to Ola John’s lobbed winner as Steaua Bucharest failed to make home advantage count. John’s wonderful finish, which just crept in at the far post, was by far the highlight of an otherwise poor match that had few clear chances at either end.
Falcao inspired Atletico Madrid to a come-from-behind 3-1 victory over Lazio in Rome.
Miroslav Klose put the home side ahead in the 19th minute before Falcao set up Adrian Lopez for the equaliser before the half-hour mark.
The Colombian forward then put the visitors ahead in the 37th minute.
Falcao added his second after the hour mark to hand Atletico coach Diego Simeone, a former Lazio player, a winning debut in the Europa League.
Jan Schlaudraff’s penalty 10 minutes from time earned Hannover a first-leg victory over Club Brugge.
The Bundesliga side, who are still unbeaten at home in their maiden Europa League campaign, fell behind to a Maxime Lestienne header early in the second half.
Substitute Artur Sobiech bundled home the equaliser after 71 minutes before Schlaudraff settled an action-packed encounter from the penalty spot.
Udinese were held to a goalless draw by PAOK Salonika as the absence of injured captain Antonio Di Natale told.
Lokomotiv Moscow took the win but surrendered an away goal in a 2-1 success against Athletic Bilbao.Iker Munain put the Primera Division side in front but second-half strikes from Felipe Caceido and Denis Glushakov (penalty), turned the tie around.
Schalke drew 1-1 at Viktoria Plzen, Klaas Jan-Huntelaar equalising Vladimar Darida’s first-half effort.
Legia Warsaw and Sporting also drew 2-2 in Poland, with the Portuguese side equalising twice through Daniel Carrico and Andre Santos after goals from Jakub Wawrznyiak and Janusz Gol.
In Holland, AZ Alkmaar edged Anderlecht 1-0 courtesy of Adam Maher’s 35th-minute effort.