Fernando Torres coolly finished off a swift counterattack to give the Blues the lead against the run of play shortly before the hour mark.
Oscar Cardozo soon equalized from the penalty spot after Cesar Azplicueta's handball but Ivanovic struck in the 93rd minute to ensure Rafa Benitez's reign at Stamford Bridge ended with silverware.
Benfica, which suffered a dramatic defeat in its virtual title-decider against Porto at the weekend, was anchored by Chelsea youngster Nemanja Matic in central midfield, while Pablo Aimar, a Spanish league winner under Rafa Benitez at Valencia, was on the bench.
Eden Hazard and John Terry were missing from the Chelsea squad due to injury so Oscar joined Juan Mata and Ramires in support of Torres, while Branislav Ivanovic partnered Gary Cahill at center back as David Luiz pushed into midfield.
If there was any despondency lingering in the Benfica ranks following its loss at the Estadio do Dragao, it did not show in the early stages.
Led by the towering presence of Matic, Cardozo, Nicolas Gaitan and Rodrigo all had chances in the opposition penalty area in the opening quarter of an hour but were denied by a combination of last-ditch Chelsea defending and a heavily watered and consequently slippery pitch.
Gradually, though, Benitez's team improved. Frank Lampard's swerving 25-yard effort seemed to have wrong-footed Artur, but after diving to his right the goalkeeper flung out his left arm to push the ball over the crossbar in spectacular style.
Bellowed on by manager Jorge Jesus, Benfica retook the initiative after halftime and Chelsea was saved by a correctly raised offside flag when Cardozo nodded home Gaitan's excellent cross from the right.
The Premier League club, though, was happy to go route one to take the lead. Petr Cech's long throw to the center circle was hooked on through the middle of the Benfica defense by Mata and Torres, after shaking off the company of Luisao, calmly rounded Artur and slotted home.
Jesus responded by reinforcing his attack with the introduction of Lima and Ola John and the change immediately paid dividends. After exchanging a one-two with Cardozo, Lima looked to flick the ball past Azpilicueta only to see the right back block with his hand.
Dutch referee Bjorn Kuipers had no hesitation in pointing to the spot and Cardozo finished decisively from 12 yards.
The Paraguayan appeared to hurt himself in taking the spot-kick but was able to carry on and forced a fine tipped save from Cech with a 20-yard volley as the final entered its last 10 minutes of the regulation 90.
Lampard would go even closer, rattling the crossbar with a terrific drive from distance, but Chelsea did not rue the 34-year-old's miss. In the third and final minute of added time, Ivanovic rose at the back post and looped home a header with Artur rooted to the spot.
The Serbian's error gifted Cardozo a glorious chance to draw Benfica level for the second time with the last kick but Cahill heroically cleared the ball to safety and delivered the trophy.
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- Rafa Benitez
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