The Serbian defender nodded home in the 93rd minute after Fernando Torres's second-half goal on the counterattack had been cancelled out by Oscar Cardozo's penalty
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 equalised from the penalty spot after Cesar Azplicueta's handball but Ivanovic struck in the 93rd minute to ensure that Rafa Benitez's reign at Stamford Bridge ended in silverware.
Benfica, who suffered a dramatic defeat in their virtual title-decider against Porto in their last outing, were anchored by former Chelsea youngster Nemanja Matic in central midfield, while Pablo Aimar, a Spanish Liga winner under Benitez at Valencia, was on the bench.
Eden Hazard and John Terry were missing from the Blues squad due to injury so Oscar joined Juan Mata and Ramires in support of Torres, while Ivanovic partnered Gary Cahill at centre-back as David Luiz pushed into midfield.
If there was any despondency lingering in the Benfica ranks following their 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.
Mata was seeing more of the ball and whipped in a dangerous cross from the left that Ezequiel Garay was able to clear with three blue shirts lurking nearby before the former Real Madrid defender was booked for cynically hauling down Oscar when it looked as if the Brazilian might drive through on goal.
Bellowed on by their coach, Jorge Jesus, Benfica retook the initiative after half-time and Chelsea were saved by a correctly raised offside flag when Cardozo nodded home Gaitan's excellent cross from the right.
The Premier League club, though, were happy to go route one to take the lead. Petr Cech's long throw to the centre circle was hooked on through the middle of the Benfica defence 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.
The 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 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 and Cech combined heroically to shepherd the ball to safety and deliver the trophy.