Benitez has proved an unpopular appointment with Chelsea's supporters but they were celebrating wildly in the Amsterdam Arena as they added this trophy to the Champions League won last season.
Fernando Torres scored against the run of play to put Chelsea ahead on the hour but Oscar Cardozo's penalty deservedly drew Benfica level.
Blues keeper Petr Cech saved superbly from Cardozo and Frank Lampard struck the woodwork in a dramatic conclusion before Ivanovic suspended for last year's Champions League final rose to meet Juan Mata's corner deep into stoppage time to prompt a subdued clenched-first celebration from Benitez.
It was a night when Chelsea rode their luck for periods against their Portuguese opponents but the sheer grit and resilience shown in grinding out this win in their 68th game of the season is a tribute to their reserves of character.
As for Benitez, he will leave Stamford Bridge following Sunday's final Premier League game against Everton a satisfied - and probably in-demand manager after guiding the west Londoners into next season's Champions League and claiming a major trophy after succeeding Roberto Di Matteo in November.
Benfica, with their greatest ever player Eusebio watching from the stands, were attempting to lift their European curse and end a 51-year barren sequence but have now lost seven successive European finals, many of their players slumping to the turf in tears at the final whistle.
Chelsea, with Eden Hazard already out with a hamstring injury, also had to do without captain John Terry for a second successive European final after he failed to recover from the ankle problem he sustained at Aston Villa.