His sparkling form comes despite a bout of food poisoning in the run up to the event, he reached the turn in his controlled second round in just 31 shots.
After failing to break par in the opening two rounds of the WGC-Mexico Championship, the two-time major champion hit the range and eventually the Internet.
Thomas closed the gap on the leaders by draining a 20-footer at the 10th and holing another birdie from much closer at the 12th, before producing a moment of magic at the 232-yard next.
Former world number one McIlroy broke his round open with a thrilling eagle on the par-four 14th hole.
And the four-time major victor was ideally placed to fulfil his part of the bargain after a second round of 65 at Chapultepec Golf Club which left him two shots ahead of Phil Mickelson, Justin Thomas and England's Ross Fisher.
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While McIlroy can reflect on a sensational round that put him in pole position to win a third WGC event, he will reflect on disappointment at the 17th and 18th, as he dropped a shot on the penultimate hole and then missed a shot putt to get to ten under at the last.
"But on the positive side I had a lot of fun with my brother carrying the clubs as he's so much fun to be around, and he did a great job today".
Mickelson had earlier showed few ill effects after being forced to change his caddie early on day two, with Jim Mackay lasting just three holes before being forced to leave the course due to a stomach virus.
"You can't replace somebody like Bones", Phil said. 6 and 7 to move to 7 under par. "I've been hitting the ball well all year, just not been putting that great", said the European Ryder Cup player.
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