Jesus will remain with Benfica until 2015, the club said in a statement.
Benfica were beaten 2-1 by Chelsea in the Europa League final on May 16, were denied the title by arch rivals Porto on the last day of the league season on May 19 and lost 2-1 to Vitoria de Guimaraes in the Portuguese Cup final a week later.
Jesus is credited with injecting Benfica with an attractive attacking style of play and is renowned for developing young talent.
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