It was the first defeat for the Blues in Europe since Liverpool knocked them out of the competition last year and was particularly galling for Avram Grant's team after they had dominated for large periods of the game.
Chelsea had in fact looked decidedly average before their opening goal was scored, only after they took the lead did they look anything like their flowing best.
Pressure had begun to slowly build before Florent Malouda was played in down the left of the penalty area and the Frenchman's low cross was deflected in by the unfortunate Deivid.
After that the Turkish side appeared, bizarrely, to relax, allowing their opponents both time and space in all areas of the pitch.
Long spells of possession preceded their first good chance of the half, after 29 minutes, when Didier Drogba was fed in the area and the Ivory Coast striker powered a hard shot at Volkan from a tight angle, but the keeper turned the effort around his near post.
Then just before half-time Drogba was played through, but with too much time to consider his options and an onrushing Volkan to worry about, the striker's effort was stopped by the keeper's legs and cleared to safety.
The Blues continued this form well into the second half, creating a number of shooting chances, the best of which was struck by Michael Ballack just before the hour and well parried by the energetic Volkan.
Yet the longer Chelsea went without finishing off the Turkish side the more dangerous Fenerbahce became, with former Chelsea man Mateja Kezman forcing Carlo Cudicini into his first save following the Serb's athletic bicycle kick.
It was still against the run of play though when Colin Kazim-Richards, the former Sheffield United forward, equalised 64 minutes in.
The substitute found himself onside and through on goal after a long ball over the Chelsea defence and he made no mistake with a vicious shot to level the game at 1-1.
Both sides looked eager for a winning goal, but it took a piece of individual brilliance from Fener attacker Deivid to break the deadlock and set up a fascinating second leg in London next week.
The Brazilian was given enough space, 35 yards out from the Chelsea goal, to look up and fire a swerving, right-footed shot into the top left corner of the net, sending the home crowd wild.