The Serbian defender, sidelined for the final against Bayern Munich 12 months ago through suspension, climbed high at the far post to meet Juan Mata's corner with a looping header that arched over keeper Artur and into the back of the net.
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The goal sent the London club's blue-decked fans into raptures and meant Chelsea became the first English club to win all three of UEFA's major trophies.
Ajax Amsterdam, Bayern Munich and Juventus are the only other teams to have won the Europa League, European Cup and the now defunct Cup Winners' Cup.
"This is a great feeling," Ivanovic told ITV Sport after the Stamford Bridge club won the 68th fixture of a marathon season.
"The team deserved this because we have had a very difficult season and a lot of games. We deserve that trophy."
Benfica, smarting from Saturday's 2-1 defeat by Porto in their domestic title showdown, started the game the brighter and Paraguayan sharpshooter Oscar Cardozo headed over from close range in the second minute.
Chelsea, for their part, had to again rely on the battling qualities that stood them in good stead in last year's victorious Champions League campaign.
The England midfielder, who became Chelsea's all-time leading scorer last weekend with his double against Aston Villa taking his tally to 203, took aim from 25 metres out and his venomous, swerving effort was tipped over the bar by Artur.
