Just as they did in last year's penalty shoot-out victory over Bayern Munich in the Champions League final, Chelsea's players carved out an unlikely win against a tough opponent. The London club now will briefly hold both trophies until Bayern meets Borussia Dortmund in an all-German Champions League final in London on May 25.
Ivanovic leapt at the far post between Jardel and Andre Almeida to send a looping header over Benfica goalkeeper Artur from a Juan Mata corner, sealing the match in the 93rd minute.
"It's a great feeling. This team deserved this, because we have had a very difficult season and a lot of games," said Ivanovic, who was suspended for last year's Champions League final. "In the end, today was a very hard game and Benfica played very well. ... We deserve that trophy."
A Fernando Torres solo effort gave Chelsea the lead on the hour mark and Oscar Cardozo levelled from the penalty spot eight minutes later — setting the stage for Ivanovic's last-gasp decider.
It was a special moment too for Chelsea's interim manager Rafa Benitez, who has faced bitter criticism from the club's own fans since replacing Roberto Di Matteo in November.
Many Chelsea fans remained angry at Di Matteo's departure, after he led the club to a first ever Champions League title. Others haven't forgiven Benitez for allegedly disparaging comments he made toward Chelsea while Liverpool manager earlier in his career.
"That was a great performance in the second half, against a very good team," Benitez said. "I'm really pleased for the players and everyone involved."
The win made Benitez only the second coach, after three-time champion Giovanni Trapattoni, to win the trophy with more than one club. Benitez first won the competition in 2004 with Valencia.
The victory also lifted Chelsea alongside Juventus, Ajax and Bayern Munich as only the fourth club to win all three European titles. The Londoners won the Cup Winner's Cup in 1971 and 1998.
However, it was a bitterly frustrating end to the night for Benfica coach Jorge Jesus.
"For most of the 93 minutes, Benfica was better than Chelsea," he said. "Benfica showed the world that they should be a worthy winner."
Chelsea won despite playing without Belgium midfielder Eden Hazard and veteran central defender John Terry, who both picked up injuries in Sunday's 2-1 Premier League victory over Aston Villa. It was the second year running that Terry had to sit out a European final — he was suspended for last year's Champions League decider and could only look on as his team beat Bayern Munich on penalties.
Terry stripped down to his Chelsea kit to join his teammates in their celebrations after the match.
"It's been an amazing time for all of us involved," said Frank Lampard who wore the captain's armband in Terry's absence." Talk about ups and downs in the last two years! But this is a big up."
The last-minute defeat in front of 46,163 fans at the Amsterdam Arena meant more heartache for Benfica, which has not lifted a European trophy since 1962 when a promising 20-year-old striker called Eusebio fired in two goals to power his team to a 5-3 victory over Real Madrid, also in Amsterdam. Since that victory, Benfica has now lost all six European finals it reached and Eusebio was on hand to watch the latest defeat.
It was a second crushing late loss for Benfica in just a matter of days. On Saturday, Porto's Kelvin scored in stoppage time for a 2-1 win that moved his team to the top of the Portuguese league with one game left.
"It was just like last week. We suffered a late goal," Jesus said. "The players felt they didn't deserve to lose, they felt like they were gunned down after the game."
Benfica was left ruing missed chances early in both halves, when the Portuguese team overpowered Chelsea, but could not convert its domination into goals.
Cardozo and Eduardo Salvio both had shots blocked in the penalty area in an 11th-minute scramble and Nicolas Gaitan fired over the bar a minute later.
Rodrigo was the next to come close for Benfica, but he slipped as he looked set to open the scoring in the 15th minute and scuffed his shot.
Artur then pulled off a miraculous save to deny Chelsea's newly minted all-time top scorer Lampard in the 38th minute.
Lampard unleashed a powerful right foot drive from outside the area and the swerving ball wrong-footed the goalkeeper, but he managed to stick out his left hand and deflect the ball over the bar.
Just after the break Chelsea again had to hang on as Benfica poured forward.
But Torres, who has struggled to find the net consistently for Chelsea since his 2011 transfer from Liverpool, finally broke the deadlock in the 60th minute.
The Spaniard collected the ball just inside Benfica's half, used his strength to turn and wrestle past Ezequiel Garay and then beat captain Luisao before rounding Artur and calmly slotting in the net from a tight angle.
He sprinted to the corner and struck a Usain Bolt-style pose in front of the Chelsea fans.
Chelsea's lead only lasted eight minutes before Cesar Azpilicueta handled the ball just inside the area and Cardozo smashed in the penalty to bring Benfica level.
Both sides had chances in the closing stages, with Petr Cech tipping over a dipping left-foot Cardozo volley and Lampard firing a long-range shot onto the bar in the 88th minute before Ivanovic's match winning header five minutes later.