Nicolas Gaitan found space on the right and his exquisite cross was headed home by Oscar Cardozo -- only for his celebrations to be cut short by an offside flag.
While the decision was the correct one, Cardozo was millimeters offside, it was the source of much frustration to a Benfica side which quickly found itself behind.
There appeared little trouble when Chelsea goalkeeper Petr Cech threw the ball out towards Juan Mata and when he failed to take control, Fernando Torres nipped in to run at the Benfica defense and coolly slot the ball home.
To its credit, Benfica refused to buckle and Jorge Jesus' side hit back within nine minutes to level when Cardozo fired home from the penalty spot following a handball by Cesar Azpilicueta.
Buoyed by its equalizer, Benfica pushed forward in search of a winner and Cech produced a fine save to push Cardozo's fierce drive over the crossbar.
But while the red shirts poured forward, Chelsea looked dangerous on the break and Frank Lampard came within inches of winning the tie after his rasping 20-yard effort smashed against the crossbar with two minutes remaining.
The game appeared destined for extra time with the scores still level going into the final minute of stoppage time.
But after Ramires won a corner on the Chelsea right, Ivanovic rose highest to meet Mata's corner and head a dramatic winner.
"It's a great feeling," Ivanovic told ITV.
"This team deserved this, because we have had a very difficult season and a lot of games.
"In the end, today was a very hard game and Benfica played very well. But we scored from set pieces and work very hard preparing that part of our game. We deserve that trophy."
It was fitting that Ivanovic should score the winner after he was forced to miss last year's Champions League final triumph over Bayern Munich through suspension.
Frank Lampard, who became the club's record goalscorer last weekend after taking his tally to 203, was quick to praise the Serbia defender and reveal he is close to signing a new contract.
"It's been an amazing time for all of us involved," he told ITV.
"Talk about ups and downs in the last two years! But this is a big up. We're a group, a team, and it was tight tonight after the long season we've had.
"No-one deserves this more than Ivanovic -- he has been fantastic. You make your own luck, and we stick together in this group. The club deserve it.
"I really, really hope to be around next year. With a game tonight and coming up we haven't sat down and signed anything, but I really hope so and things are looking good. The club have been brilliant."
For Torres, it means he is now a reigning World Cup winner, European Championship winner, Champions League winner and Europa League winner -- the first for any player.
"I am very happy," the Spain international told ITV.
"It was a very tough game, and Benfica were much better in the first half. The first half was not good enough at all. We really wanted to win this Europe League, and maybe this was going to be our only chance."
This defeat caps a miserable week for Benfica, which looks set to lose out on the Portuguese league title following a dramatic late defeat by rival Porto.
Benfica has now lost its past seven major European Cup finals -- all of which have come since being hit by the infamous "Bela Guttmann curse".
Guttmann, a Hungarian coach, led Benfica to glory in the European Cup, winning the competition in 1961 and 1962.
But after his request for a pay rise was turned down by the newly elected president Antonio Carlos Cabral Fezas Vital, Guttmann placed a curse on the club and declared it would not win the European Cup for another 100 years.
Not even the great Eusebio, one of Benfica's most famous sons, was able to help lift the curse when he visited Guttmann's grave before Benfica's defeat in the 1990 European Cup final.