The young Spaniard was forced to wait out an 85-minute delay when play was suspended mid-round due to heavy rain, but never let up on his charge up the leaderboard. He fired a 9-under 63 to overcome a six-shot deficit and tie Els at 20-under 268.
Garcia took care of business on the first extra hole, the par-3 16th, holing a chip from 23 feet out to capture the title and the $2 million first prize.
'I played it perfectly. It was downhill with a left-to-right break and I hit it one-cup left,' said Garcia of his chip-in. 'I wasn't happy yet because I knew Ernie could still hole his putt for birdie.
Els did not make his birdie to extend the playoff, giving the 21-year-old the win in this 12-man field.
'It's been a great year for me,' said Garcia, who also won twice on the PGA Tour in 2001. 'Last year was really tough and to be able to come back and play this well was wonderful.'
With the playoff loss, Els closed out the 2001 campaign winless worldwide, breaking a streak dating back to 1992. Ealier in the year, he also saw his streak of seven straight seasons with a win on the PGA Tour come to an end.
Garcia started hot, hitting a wedge from just outside 100 yards for an eagle on the par-4 third. He added birdies on seven and nine to make the turn at 15-under before going on a tear on the back nine.
Garcia made six birdies over the final nine holes to climb to 21-under, but ran into trouble on the 18th when his approach found the rough to the right of the green. Garcia chipped out within 18 feet. but missed for a bogey.
'I thought I'd lost it on 18,' said Garcia. 'I was trying to cut an 8-iron into the green, but sometimes, under pressure, you get a bad swing and I lost it right.'
Els held the lead for all three rounds coming into Sunday, but nearly lost the tournament altogether when he dropped to 19-under with a bogey the 11th just before the sirens sounded. He birdied the par-5 14th to match Garcia at 20-under and made a critical par after a poor drive on the 17th hold the tie.
The South African, playing for a record third consecutive win in this event, needed a birdie on the final hole for a win but managed only a par.
Bernhard Langer, a two-time winner of this event, finished third at 17-under 271, followed by Canada's Mike Weir at 16-under 272.
Full-field scores from the Nedbank Golf Challenge