Playing his first round as a Major Champion after his triumph at the U.S. Open Championship, Rahm was looking to regain his title as king of the Rolex Series with a fifth win in the European Tour's blue riband events.
He made seven birdies and two bogeys in a 66 that left him just two shots off the lead, but that was a shot behind Thomas who was bogey free in a 65.
Rory McIlroy, a four time Major Champion, completed a group comprised entirely of Major winning World Number Ones, and Rahm revealed being in such company was a spur to go for greater things.
"Playing with Justin Thomas and Rory McIlroy with their resumés puts you in your place," he said. "I'm still really far from what they have accomplished. It's certainly motivational, you know?
"I was able to accomplish a dream, something that some people have taken longer to do and to do it at 26, playing some good golf, it's good stuff.
Playing with Justin Thomas and Rory McIlroy with their resumés puts you in your place
"It's all a motivation to keep playing better and win the tournament.
"I'm not going to lie, I think I might have missed that first tee shot because I'm there sitting with Rory - great player, JT - great player, and I get announced as World Number One, Race to Dubai leader and U.S. Open champion.
"They just said Rory McIlroy, JT, so I was just a little surprised by it. I didn't expect it. My ego might have got a little too big, tried to hit a little too hard on one.
"I didn't have my best feel out there but after the first tee shot, which was probably about as bad a tee shot as I can hit - feeling-wise as well - I just told myself really trust the visualisation process, see the shot, trust the shot and trust that your body can do it, and it really worked out.
"Sometimes you've just got to get out of your own way."
The highlight of Thomas' round was a remarkable 90 foot putt for eagle on the seventh as he looks for a first Rolex Series title.
"That was a steal," he said. "You obviously never plan on making a 100 footer or whatever it was but the hole got in the way perfectly.
"Obviously, six under is great. I'd love that every round of golf I play. Bogey free made it pretty stress free.
"I was a little upset or disappointed with some of the iron shots I hit. Felt I could have hit them closer but nice to play that last hole as well as I did to hopefully generate some momentum.
"The speed of the greens, I think all of us had a hard time getting them to the hole on some of them. So just getting accustomed to that. I felt like a couple of putts, if I would have had the speed correct, I would have made.
"Overall, drove it well. Had a couple drives that were loose but for the most part just a solid day.
"Jon and I were kind of feeding off each other a little bit and just trying to stay in the tournament."