Cooper, a former print and radio journalist, worked for ISL under 1992, first as events manager and later as vice-president of their football division.
He joined FIFA as communications chief in 1995 but was a shock casualty as Blatter went about clearing out various figures following his landslide victory in May.
UEFA have confirmed Cooper will be leading the Jubilee 2004 project, as well as planning the series of special events that will take place to mark UEFA's 50th birthday.
Said Cooper: "I am very glad to be joining UEFA, and to have the chance of leading this major project to celebrate 50 years of UEFA's existence and the growth of football in Europe.
"I am looking forward to returning to work in the football environment and to the opportunity of working with the team at UEFA."
Added UEFA chief executive Gerhard Aigner: "I am very happy to have someone of Keith's ability and reputation joining us to head-up this project.
"His knowledge and experience of the game of football at world level will help us to create a series of events and celebrations that will make UEFA's 50th year of existence in 2004 a memorable one."
The reasons for Cooper's departure at FIFA were never elaborated upon.
Speaking to sportbusiness.com
Former FIFA communications director Keith Cooper - ditched by soccer's world governing body following Sepp Blatter's re-election - has agreed terms with UEFA to take charge of its 50th anniversary celebrations.
