The World Matchplay final will act as a Rugby World Cup 'preview' of sorts, with Els's South Africa and Cabrera's Argentina set to face off in a semi-final in France later on Sunday.
Els, visibly weary after his victory, said he was excited by the 36 hole final against Cabrera.
"It's been a long tough week, but this is what you play for and it's really satisfying to get there," the South African said.
"I'm a little drained and I had to dig really deep to stay ahead of Henrik."
Six hours into the match Els sunk a five foot putt on the seventh green to go ahead for the first time, before sinking a six-footer on the ninth green, putting daylight between himself and Stenson as the six time champion, who took just 31 on the outward nine, moved to three up, with nine to play.
"I worked on my game all the time and that's why I love 36 hole match play, because you have to play well all day."
However Stenson lifted his game, striking back on the par three 10th by holing a 23 foot putt for a birdie.
Nervousness and fatigue from both players became increasingly evident, until Els holed a key putt on the 15th green, leaving him three ahead with three to play.
The Swede responded gamely on the 16th by attacking the flag, but was unable to hole his 14 foot putt to win the hole.
"Mentally, this game tests you so much," Els said.
"Today, with persistence, I got through it. I worked on my game all the time and that's why I love 36 hole match play, because you have to play well all day."
Angel rises above Hunter
Argentina's Angel Cabrera held off a late
comeback from Hunter Mahan [GALLO/GETTY]
Meanwhile Cabrera, six up after 22 holes, appeared to cruising to victory in his battle with Mahan, but a sudden flurry of birdies from the American forced the Argentinian onto the back foot.
By the time the pair walked off the 10th green, the Cabrera's nerves were fraying after Mahan had cut his lead to just two holes, following a purple patch with his putter.
"I played with Mahan in Augusta when he was an amateur, so he didn't surprise me because he's a very good player," Cabrera said.
"I tried to stay focussed. I needed to stay calm and I did."
Mahan finally succumbed on the 17th green when he could only halve a hole he had to win, despite sinking a birdie putt from 12 feet.
"He was just a little better than me today," Mahan said.
"I battled hard but I can't be too upset. I just wasn't as sharp as him or as good as him for the first 21 holes."