Istanbul got the vote over five other venues, including the Stade de France and Atletico Madrid’s Vicente Calderon. It is the first time a Turkish city has been awarded the honour of staging a major final.
The 80,000-capacity Ataturk Stadium will host Europe's biggest game of the season, with UEFA claiming security concerns had been met.
This comes after the missile-throwing incidents during Turkey's Euro 2004 qualifier against Macedonia in Istanbul in September, and the poor behaviour of Besiktas fans when their group game with Chelsea was switched to Gelsenkirchen in Germany.
With thoughts still fresh over the murder of Leeds fans Kevin Speight and Christopher Loftus in Istanbul four years ago, UEFA's decision was met with a degree of shock.
John Boocock, chairman of the Leeds United Supporters Trust, said: "Football fans should be able to go to watch matches anywhere in the world with a guarantee of their safety and I don't think the Turkish football or government authorities can give that guarantee.
"That's been proved on a number of occasions and giving this game to Istanbul is an insult to the poor lads who died there.
"The type of activities we saw in the Ali Sami Yen Stadium would have seen Elland Road shut down if they'd happened here.
"There seems to be one set of rules for English fans and another for the Turks. I'm sure that across Leeds there is now a feeling of real shock."
Simon Jose, of the Leeds United Independent Fans Association, added: "UEFA have either shown no sensitivity at all or they are completely naive.
"I can't believe that Turkish policing will improve to the standards of Holland or Portugal in 18 months and this shows they're not interested in listening to what real fans think."
UEFA have chosen Sporting Lisbon's Jose Alvalade Stadium to host the UEFA Cup Final.