Cameron Smith of Australia set the pace with a bogey-free eight-under 64, while Keegan Bradley, Xander Schauffele and Poom Saksansin of Thailand stood a stroke off.
Smith, 24, victor along with Jonas Blixt at last April's Zurich Classic of New Orleans, made eight birdies in his first start of the new tour season.
Twenty-five-year-old Matsuyama, another sparkling young talent, was runner-up behind Thomas in Malaysia last year in a breakout season boasting three wins and two top-five finishes at the majors.
Brendan Steele, coming off a victory last week at the Safeway Open, had an opening 67 to be three shots off the lead. "Today's round was really the first time I've picked up a club since the Presidents Cup, but hopefully I can find my game quickly and somehow make it interesting on Sunday", he said at TPC Kuala Lumpur on Tuesday. "I pretty much tried to copy everything he did because I figured he's a good guy to imitate out here". Now instead of struggling for starts he has a three-year exemption and is embarking on a three-week stretch of no-cut events in Asia. The last player to win his first start in a tour event was Jim Benepe at the 1988 Western Open.
Thomas was in tied 23rd place and other favourites also fared badly at the PGA Tour event in Malaysia, with both Japan's Hideki Matsuyama and India's Anirban Lahiri trailing the leaders.
"It was boring, which I guess is a good thing out here", said Schauffele, who was paired with Thomas in the opening round. The Thai is one stroke behind Cameron Smith after the first round of the CIMB Classic.
Kevin Na nailed a 45-foot putt for a birdie at the 15th and then holed an iron for an eagle at the 16th but bogeyed the last to drop to a share of fifth with fellow Americans Gary Woodland and Pat Perez after carding a 66. Among those with 67s who are tied for eight are Brendan Steele, last week's victor at the Safeway Open, and Davis Love III.