| Needing to make a birdie at the par-five finishing hole to force a playoff with the Spaniard, Schwartzel hit his second into the water right of the green. He managed to make par for a 72 and second place on 12 under.
Lee Westwood finished third on nine under.
It was a dramatic end to a tournament that seemed destined to head the way of Schwartzel before an unheralded 23-year-old Spaniard from Cadiz who never gave himself a chance upstaged the young South African.
'What can I say, I am the best for one week,' said a delighted Quiros, who won in his rookie season on the European Tour after graduating via the Challenge Tour.
'At the beginning of the round I didn't think I could win. Schwartzel has won before on this course and was playing in front of his home crowd. I was very nervous,' said Quiros, who started the round four strokes behind leader Schwartzel.
Schwartzel's hold on the tournament saw him take a two-stroke lead into the final round. But the rest of the field quickly challenged him.
Ryder Cup star Lee Westwood made a run at Schwartzel early on, but the putts refused to drop on the back nine for the Englishman.
Quiros made the most significant charge over the closing holes. His three successive birdies from the 13th gave him the sole lead as Schwartzel stumbled with bogeys at the ninth and 10th holes and struggled to make anything happen in his round.
But the young South African enjoyed his first break at the par-five 15th. His drive pitched out of bounds, but then bounced twice on the small stone wall acting as the boundary before dropping in bounds. Schwartzel went on to make a crucial birdie there, and followed it up with another at the 16th to tie Quiros for the lead on 12 under.
But Quiros, a man known for his aggressive style of play, made a bold birdie at the last. After lipping out for eagle with a 65-foot putt, he tapped in for birdie to set the mark at 13 under.
Playing conservative golf all week, Schwartzel went for broke with his second and instead found the water.
'I had quite a hanging lie and came off it a bit. I was going for the middle of the green but just hit a bad shot,' said Schwartzel.
'It's not nice. I was leading from day one. It's not a case of nerves. I just hit a few bad shots.
'There was nothing happening with my putting up until I got extremely lucky on 15. Things changed there and all of a sudden I holed two putts out of nowhere. I made two great birdies at 15 and 16. Then you all saw what happened on 18.'
Defending champion Ernie Els finished the week tied eight on six under.
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