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Watson finished one stroke clear of Jason Kokrak and former Masters champion Adam Scott.
Overnight leader Watson had 10 players within three shots of him going into the final round. In 2014, when he last won the LA Open, Watson went on to win the green jacket at Augusta. “To win in a tough way means a lot . . . for me is it is about staying patient,” said Watson, after his ninth PGA Tour win.
Playing in the tournament for the first time McIlroy opened rounds of 67, 69 and 67 and made a real statement of intent on the final day with an opening eagle on the on the Par 5 first.
But McIlroy then signed for seven bogeys – including a run of three successive dropped shots from the 11th – and only salvaged a closing round 75 with a birdie on the 18th.
Adam Scott – who had an electrifying start that included an eagle and three birdies in his first six holes to card a 67 – with Kokrak – chasing a maiden tour win – and Dustin Johnson became the main players in the drama.
Australia’s Marc Leishmann and KJ Choi of South Korea carded 69s to finish tied in fifth place. McIlroy’s tied-20th finishing position was disappointing.
The Holywood man now heads back to the east coast for this week’s Honda Classic at Palm Beach Gardens and next week’s WGC-Cadillac championship in Doral.
Pádraig Harrington's triple bogey seven on the Par 4 seventh proved very costly as he signed for a closing 75 for two-under-par finish T45th.
Harrington defends his Honda Classic title in Florida this week, where Shane Lowry and Graeme McDowell will also be in the field.