كتب : Hatem Maher
Josu Sarriegi stunned the home crowd nine minutes past the hour mark to notch the winner.
Inter's Brazilian keeper Julio Cesar did well to block Ioannis Goumas' free header but the ball fell to the path of the unmarked Sarriegi, who stabbed home from close range.
In the other Group B game, Werder Bremen came from two goals down to earn a 2-2 draw at Cypriot side Anorthosis Famagusta.
Substitute Nikos Nikolaou broke the deadlock in the 62nd minute and Savio doubled the lead six minutes later.
A penalty by Brazilian playmaker Diego on 72 minutes narrowed the gap before Hugo Almeida secured a share of spoils three minutes from time.
Italian champions Inter are in charge of Group B on eight points, one ahead of second-placed Panathinaikos.
The Nerazzurri are three points clear of Anorthosis while Bremen lie at the bottom on four points.
Inter guaranteed a place in the next round while Anorthosis will vie with Panathinaikos for the second qualifying spot when both sides meet in the last group stage game.
Bremen will be hoping to secure a UEFA Cup berth after losing hopes of reaching the Champions League round of 16.