A two-goal lead should be sufficient for Middlesbrough to progress when they go to Greece for the second leg on September 29, yet there was little in the way of drama to excite the fans on a cold night on Teesside.
Boro failed to hit the form they displayed in their Premier League win over Arsenal and at one stage in the second half, the visitors threatened to draw level.
Former Middlesbrough star Emerson received a warm ovation from the home fans before the game, as he lined up for the Greek side. The supporters obviously remembered the flamboyant Brazilian star from an exciting spell at the club that included two Wembley finals.
There was limited penalty area action in the opening 25 minutes, as neither side could turn their passing play into clear chances.
Middlesbrough, however, went ahead in the 28th minute after Petr Pizanowski could only punch out a Massimo Maccarone shot as far as George Boateng, who made no mistake with the straightforward finish.
The visitors began the second half with more threat and confidence, while Boro lacked a sense of urgency and for a period lost out in midfield.
Stavros Labriakos shot wide with an excellent chance after 55 minutes and shortly afterwards fired inches past the post.
Emerson sent a drive narrowly over the bar and there was a threat Middlesbrough could pay for their lack of authority.
Former Portsmouth striker Yakubu, who scored his first goal of the season against Arsenal, was among the substitutes introduced by Steve McClaren in the second half.
Yakubu came close to increasing Boro's lead following a right wing cross from Doriva, but the Xanthi keeper saved his header.
The hosts clinched victory seven minutes from time when Mark Viduka, recalled to the starting line-up, scored a fortunate goal.
Defender Jacques Paviot had the misfortune to deflect the Australian's effort past his own goalkeeper to all but seal Boro's place in the group stage of the competition for a second consecutive season.