Sterne carded an eight-under-par 64 for a tournament total of 260, seven shots ahead of second-placed Charl Schwartzel.
After finishing second in the Dubai Desert Classic last weekend, Sterne got his reward for some consistent golf that featured just one dropped shot in his four rounds at the Royal Johannesburg and Kensington Golf Club.
"It was a pretty special day, I played really good golf all week," Sterne said at the presentation of the trophy. "I only had one bogey all week and that was key to scoring well.
"It's quite tough coming from a good week into another week, you do expect to play well. I got off to such a good start on the West Course (on Thursday) and having won here before I felt comfortable."
Sterne went into the final round tied on 19 under par with compatriot Trevor Fisher Jnr, but the latter carded a disappointing 73 to finish in tied-sixth position.
Schwartzel birdied 17 and 18 to card a 66 to take second place with a 20-under-par tournament total of 267. That took him ahead of Portugal's Ricardo Santos, who matched Sterne's round on Sunday with a 64 to finish his tournament on 19 under par and tied third with George Coetzee (67) and Chilean Filipe Aguilar.
The 2013 Joburg Open is Sterne's sixth European Tour victory and moves him into the top 60 in the world rankings ahead of the WGC-Accenture Match Play championship in Arizona starting on Feb. 20.
It is the second time he has won the tournament, having claimed the trophy in 2008, but he said that two years spent out of the game made him worry whether he would ever make it back on to the professional circuit.
"It crossed my mind a few times. I didn't think I was going to be out for so long but six months became a year, then almost two at the end of the day," Sterne said.
"The only thing that kept me going was all the other South Africans, they kept winning lots of events and I thought to myself if they can do it, so can I."
The 31-year-old hopes that his solid start to the year will allow him to return to the majors in 2013.
"It's a big year for me hopefully, especially after such a nice start. I hope to get back into the majors, that's where I want to be playing and competing on that stage."
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