Lonard, the 1997 champion, closed with a 6-under-par 66 to catch Coles (70) and Scott (71) at 9-under 279. Lonard started the day five shots off the lead held by Scott.
The victory gave Lonard a spot in the Masters in April and a place in the top 50 in the world rankings. Lonard made 23 of 24 cuts during his first season on the PGA Tour, where he finished 41st on the money list with more than $1.4 million.
Scott was eliminated after the first playoff hole when he failed to make a par putt. Lonard and Coles parred the second extra hole. But Lonard won with a par on the third after Coles made a bogey after going into a fairway bunker with his tee shot.
Last week, Lonard and Jarrod Moseley were declared champions of the Australian PGA when darkness cut short their playoff after one hole.
Final scores from the MasterCard Masters