The Spaniard shot a 4-under 68 to total 19-under 269.
Former British Open champion Paul Lawrie (67) was second, a stroke ahead of a group of three players that included Sweden's Karlsson (71).
A thunderstorm Saturday had forced the leaders to finish their third round Sunday.
Karlsson, who started the final round trailing Quiros by one stroke, fell three behind at the 10th when Quiros sank a 7-foot birdie putt.
Karlsson leads British Open and PGA Championship winner Padraig Harrington and Lee Westwood of England in the Order of Merit, with only next week's Mallorca Classic remaining before the season-ending Volvo Masters.
England's Ross Fisher (71) and Steve Webster (68) joined Karlsson in third, while Westwood (68) was tied for 16th.