The 41-year-old thwarted a strong finish from good friend and fellow South African Retief Goosen to secure a one-shot triumph in the European Tour event at the Durban Country Club on Sunday.
Els claimed his fifth victory in the tournament thanks to a closing 66 and Goosen stayed hot on his heels until the end with a matching six-under-par effort in the final round.
"It was one of the most incredible days I've ever had in my 20 years as a professional golfer," said the world No 12. "In the morning round we shot a better-ball score of something like 58 and the lead changed hands quite a few times. This win really means a lot to me."
Heavy rain meant organisers reduced the competition to 70 holes after the weather rendered the par-3 fourth unplayable. The decision meant Sunday's final two rounds were contested on a par-69 course instead of par-72.
"It was a great championship for South African golf," added Els in a reference to the third and fourth place finishes of British Open champion Louis Oosthuizen and Charl Schwartzel. "Of course all wins are special but this means more than most as it is our national championship."
Els, winner of the US Open in 1994 and 1997 and the Open Championship in 2002, ended a two-year victory drought by lifting the WGC-CA Championship in Miami in March. He triumphed again at the Arnold Palmer Invitational in Orlando at the end of March but had to wait until the PGA Grand Slam of Golf in Bermuda in October for his next win.
"It was in many ways a season of two different halves for me," said Els. "I came out of the blocks pretty fast and won twice in March during the Florida swing but after the US Open (in June) my game went off the boil for most of the summer.
"I must admit it was a struggle to get things back on track but during the last five or six weeks of the season there were signs the hard work I'd been putting in was starting to pay off."