Uefa has also decided to centralise the sale of broadcast rights to the competition, which has been overshadowed in recent years by the more prestigious and lucrative Champions League.
The number of teams will be increased from 40 to 48, and the group stage changed from eight leagues of five, playing each other just once, to 12 leagues of four, playing each other home and away.
The Uefa Cup was introduced in the 1971-1972 season to replace the Inter Cities Fairs Cup and has been the only European club competition to rival the Champions League since the Cup Winners' Cup was dropped in 1999.
Efforts to revitalise the competition have already been made, such as the introduction of a group stage, but the Uefa Cup has struggled under the perception it is a second-rate event compared to the Champions League.
This perception is compounded by the fact that clubs who have failed to survive the group stage of the Champions League continue in the Uefa Cup.
Michel Platini, the UEFA president, said: "These changes will improve this historic competition which is very important for Uefa and for European football, as it gives more fans, players and clubs the thrill of European club football.
"I am convinced the new format will give the Uefa Europa League a successful new impetus."
In the UK, this season's Uefa Cup is being aired by Channel Five and satellite broadcaster Setanta, who share coverage of matches involving British clubs Tottenham Hotspur, Manchester City, Aston Villa, Everton, Portsmouth and Motherwell between them.