City qualified through the same route in 2003 and manager Sven-Goran Eriksson was delighted with the news after the Blues narrowly missed out on securing European qualification through their league finish.
"It's like the dream came true!" he told the City website.
"Our dream to play in Europe has been strong all season. At one point we thought we were almost sure to get there, at other points we've been almost out of it, but now this news is absolutely fantastic for the club, the fans and for everyone.
"It's a step in the right direction because the target for this club in the future is to play in the Champions League, and the UEFA Cup is a very good school to learn about European football," Sven added.
"It's a confirmation that we are a good team, but also a team that behaves well on the pitch. We are good with referees and we try to follow the rules as much as possible. It's like a bonus for us."
City owner Thaksin Shinawatra added: "I am delighted for everybody at the club, especially our suporters."