McIlroy will at least have the consolation of some desired extra time off before stepping up his bid for a first Masters title at Augusta National, which would make him the sixth player to complete a career Grand Slam.
But he was three down after six holes to compatriot Watson and lost 3&2.
The 39-year-old Watson was one of four remaining players on Sunday.
Both will now try to regroup with the first major of the year, the Masters, two weeks away. I got off to a bit of a scrappy start today. "Physical strength, being healthy, is going to create the mind - you're going to have confidence".
"I was 50/50 on Monday", Thomas said. 'I made a lot of key putts, par savers, to keep me running smoother on the back nine. Just played solid golf tee to green.
Dustin Johnson didn't win a match this week and will not get any world ranking points.
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Asked how he felt going into the weekend, Thomas replied, "The same as the other 16 guys".
"I haven't had such a hard time not thinking about something so much". And that really sucked, " Thomas said.
"Probably nothing different from what I've been doing", Stanley said of his mindset for opposing the reigning Masters champion.
"You're constantly getting questions about it with the media but I need to be mentally stronger than that, and understand that it's just a match". DJ did turn heads, however, with a 489-yard drive on the 12th hole that would have been a Tour record (by 13 yards!) if statistics counted at the Match Play. At the second, Kisner missed a nine-footer for par, falling 2-down for the first time all week.
"It's just one of those deals".
Kisner will look to build off that dominant outing Sunday with a spot in the finals on the line. His last hope was on the par-5 16th, and his second shot went through the green and onto a dirt path with a boundary fence right behind him.
However, Watson bounced straight back to birdie the 10th and although he left a putt short from five feet to win the next, Thomas found water with his approach to the 12th and missed good birdie chances on the next two holes. Moments later, he received a text that he needed to win his match against Kisner. "He kept hitting it in there close".
"But then I can't stay out of the country too long as I have to get dressed-up and be ready to return to Augusta".