The trophy means Rafael Benitez’s short reign as Chelsea’s interim manager will have a happy ending, as fans celebrated their second European trophy in as many seasons wildly.
Fernando Torres finished of a swift counter-attack to open the scoring on the hour mark.
Benfica coach Jorge Jesus bolstered his attack, bringing on Rodrigo Lima and Ola John, and the change paid off immediately.
Lima played a one-two with Oscar Cardozo, and then tried to flick the ball past Cesar Azpilicueta, who blocked the ball with his hand. Referee Bjorn Kuipers pointed to the spot and Cardozo equalised.
Petr Cech had to make a superb save ten minutes from time off a dipping volley from Cardozo, to keep the Blues in the game.
Three minutes from time Frank Lampard thumped the woodwork, before Ivanovic’s dramatic winner.
The Serbian defender timed his run perfectly and rose to head home a corner by Juan Mata deep into stoppage time.