The Serbian defender headed home in the 92nd minute to secure the title for the Blues and break Benfica hearts in the process.
It was another cruel blow to the Portuguese club, who lost to rivals Porto in similar circumstances last Saturday, which saw them fall to second place with only one round remaining.
Chelsea can now add some Europa League silverware to its trophy case after winning the Champions League last season.
It was Benfica who fired the first warning shot in Amsterdam as Oscar Cardozo headed over the bar just two minutes into the encounter.
The Portuguese outfit dominated proceedings in the early going but could not find the opening goal they rightfully deserved.
Frank Lampard, who broke Chelsea’s scoring record last weekend, almost found the opener when his wicked shot was pushed over the bar by Artur.
Benfica must have been disappointed with the 0-0 scoreline heading into the half-time interval but it was still anybody’s game.
The Portuguese club picked up where they left off as Cardozo thought he had given his side the lead but his goal was ruled out for offside.
But it was Chelsea who scored first as Fernando Torres latched on to Juan Mata’s flick, held off his marker and found the back of the net from an acute angle.
It was 1-0 to Chelsea but Benfica was soon back on level terms as Cardozo made no mistake from the penalty spot after Cesar Azpilicueta was whistled for a handball.
Torres was making a nuisance of himself once more and had a strong penalty claim denied before Cech was forced to make a huge stop on Cardozo.
It was end to end stuff and wonderful viewing for the neutral with extra time looming. However, an extra 30 minutes was not needed as Ivanovic’s looping header from Mata’s corner sent the Chelsea fans into a frenzy in the 92nd minute.
It was a cruel blow to Benfica but Chelsea had won the Europa League thanks to Branislav Ivanovic’s last-gasp header in what was an enthralling contest.