"Your buddies, those are the people you want to lose to least," a smiling Fowler told Golf Channel after a six-under-par 65 at Scottsdale TPC.
He posted a 13-under 129 total, one in front of Thomas (66) and two clear of South African Branden Grace, whose 64 was the best score of the round.
Fowler was frustrated by his putting for much of the round, missing a series of short putts before things finally clicked over the closing holes.
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"I had a chance to birdie the last seven," he said after knocking in a 10-footer at the last.
"I hit some really good putts to finish the day off."
Fowler lost a playoff at the event in 2016, and was the 54-hole leader last year, but is yet to win the tournament, which is renowned for its enthusiastic and vocal gallery.
"I love how loud it gets here," said the 30-year-old.
"There's still some people out there that say some dumb stuff, but it's going to happen."
Fowler and Thomas will play in the final group on Saturday, and will probably car pool to the course again.
"Anything with Rickie around here is going to be pretty bizarre," said Thomas, a nine-times PGA Tour winner, referring to the likely amped-up nature of the gallery.
Thomas was disappointed to give up three shots to Fowler over the closing stretch.
"I played well the first 15 holes," he said. "I'm a little disappointed with the last three."
(Reporting by Andrew Both in Cary, North Carolina; Editing by Greg Stutchbury)
