Eight-time WGC-Bridgestone champion Tiger Woods dropped three shots after a 73 to plummet to three under.
McIlroy figured to be Thomas' most prominent roadblock on his way to his first World Golf Championship bottle cap, but the Northern Irishman tumbled out of contention when he played a six-hole stretch around the turn in 4 over par.
A red hot Johnson picked up another shot at the 10th, but his progress was halted by a string of pars in Akron, Ohio, where Kyle Stanley joined him on 11 under through 10.
Day signed for a 73 to sink to a share of 10th at seven under, while Leishman also carded 73 to finish a shot back in a tie for 14th.
Playing two groups in front of Perry, Short got within two shots with three holes to go, but Perry made a birdie putt at 16 for a three-shot cushion. He made just a single bogey - at the sixth hole - and cruised to a closing 69 for a four-stroke victory.
Woods opened with a bogey, bounced back with three birdies over his next four holes and looked like he might make a move with his birdie on the 12th.
Thomas captured his first World Golf Championship and heads to his title defense at the PGA Championship with plenty of momentum.
Bhullar holed a 40-yard chip for eagle on the par-5 17th at Natadola Bay Championship Golf Course.
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The only regret for Thomas was a mistake that didn't cost him as much as it could have.
"The course was a lot tougher today and I just completely lost it on the last six holes".
"We were lucky to get up-and-down for 6, but that was a stupid decision", Thomas. "So tomorrow is going to be one of those days I'm going to have to go out there and post a low one and see what happens".
Johnson, the No. 1-ranked golfer in the world, earned $510,000 for his efforts on a sunny day with temperatures in the 90s in Akron.
"I felt better with my game than I did yesterday, for sure", he said.
"I needed to go get it today and I didn't do it". Paul and Phyllis Thomas live in the Louisville, Ky., and this is the first time they saw Justin win in person on the PGA Tour.
"Very similar to, you know, the first day".
The US PGA Championship - the final major of the year - begins on Thursday. 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. Woods did not dispute the fact that before each of the 12 tournaments he played this year before the Bridgestone, he spent some amount of time practicing the week before the event.