Stenson played an on-par final round -- his worst of the tournament -- for a 17-under-par 271 to beat South Africa's George Coetzee, who at one point was tied with the Swede in the lead.
The Swede's performance had fallen steadily since his last victory at the 2009 Players Championship, when he was ranked world number four.
"When it takes that long between wins you wonder if there will be another.
You've just got to fight hard and put the work in. In this game you need to put a lot of effort in to get something back. I'm very relieved to have won this one," said the 36-year-old in Ekurhuleni east of Johannesburg.
His victory at the tournament, co-sanctioned by the European and Sunshine tour, books his space in the Race to Dubai, where he is 45th on the list. The cut-off is 60.
"I was 59th in the race to Dubai so I needed a good week," he said.
His current world ranking at 113 will also now improve.
After a steady lead in the first eight holes Stenson double-bogeyed the par-three ninth, when his tee shot went into the water. Coetzee parred the hole to share the lead.
"I knew it wasn't going to be easy. There was a firm breeze out there and I had a few guys on my tail. Then I threw two shots away on nine. But I wasn't panicking. I felt I had to keep playing my own game and try and produce chances out there," said Stenson.
The par-three 15th hole became the decider when the 26-year-old South African's turn came with a double bogey. He ended with fourteen-under-par 274.
Stenson birdied the 16th and the 17th to widen his lead to three strokes, finishing the 18th on par as late-afternoon raindrops started to fall.
"I played aggressively coming in and made the birdies, and luckily George didn't. But George played well and will get that win sooner or later," said the winner.
His victory in the 102nd edition of the world's oldest championship after the British Open had a special meaning after 12 worldwide and six European tour titles, he said.
"I've won some great tournaments in my career but winning these traditional championships is always special. It's very humbling to get your name on a trophy that has so many great champions. Gary Player is on there 13 times, and I'm not sure I'll be able to match that," he laughed.
South Africa's Thomas Aiken tied for third place with former world number one Martin Kaymer from Germany, with thirteen-under-par 275 after the final round.
Masters 2011 champion Charl Schwartzel, also from South Africa, sunk seven birdies to end fifth with five-under-par in the final round and a 277-total.
Defending champion Hennie Otto meanwhile equalled Coetzee's Saturday course record of 63 in his final round. The improvement on his 71, 72, and 75 in previous rounds pulled him to a 280 total, nine behind the winner.
It was a dismal day for Sweden's Magnus A Carlsson, who was tied with Coetzee in second at the start of the round, but shot four over par to end sixth with 279.
Branden Grace, currently sixth in the Race to Dubai after his four European Tour wins this year, ended eight-over-par with 296.