Thomas had a couple of early setbacks but was commanding thereafter, plotting his way round the treacherous terrain so efficiently that he shot a 67 and finished with a three-stroke lead at 14 under par.
But it will be McIlroy who will partner Thomas in the final group on Sunday, with the 29-year-old having now strung together 26 holes without a bogey.
With a hectic schedule coming up - Woods is expected to play four of the next five weeks - there is little time for him to work it out in practice. He would make just one par on the back nine to go along with three birdies, three bogeys and two double-bogeys for a four-over 40.
With the US Tour changing the event's name and moving it to Tennessee next year, the 14-time major winner's hopes of farewelling Akron, Ohio with a first worldwide win in five years are all but over.More news: CDC Report: Hundreds Ill From Parasite In McD Salads
Players Championship victor Webb Simpson holed a wedge from 111 yards for eagle at the par-five 16th and joined Woods on six-under in the World Golf Championships event. The World Series of Golf began in 1962, and it became an official PGA Tour event in 1976. Stanley closed with a 68. Johnson bogeyed the last hole for a 64 and shared third with Thorbjorn Olesen of Denmark, who also had a 64.
Fleetwood, the runner-up at the U.S. Open, was most pleased to see nothing higher than 4s on his scorecard.
The Holywood man, who won here in 2014 as part of his dominant stretch that also saw him win The Open and US PGA Championship, got off to a strong start after birdieing the second despite a wayward drive which finished on the adjacent third hole, and the four-time Major victor was then nearly hit by a shot from the group in front who were actually playing the par-four.
McIlroy won at Bay Hill in March and has three runner-up finishes, and he had said Saturday afternoon he was exhausted of finishing second.More news: China won't accept US trade 'blackmail': state media
It was a different scene from two weeks ago when Woods was in the thick of contention at The Open, leading with eight holes to play before a tie for sixth helped him qualify for the final WGC event at Bridgestone.
Thomas, who defends his title next week in the PGA Championship, goes after his third victory of the season, but first in five months. He got an unlucky break at the first hole when his approach shot hit the flagstick and clattered off the green, which set the tone for a 74 that left him seven shots back.
"Everything. I didn't warm up very well, I didn't hit the ball crisp or clean".
"I just didn't hit it as sharp as I would have liked", Woods said. "I got a little choked up when I saw grandma and grandpa over there". "I was 1 under standing on the 17th tee and I think if I had to finish 1 under, it would have felt like the worst I could have shot today".More news: Suspected Russian spy found working at United States embassy in Moscow
This article was written by Doug Ferguson from The Associated Press and was legally licensed through the NewsCred publisher network.