With gusting winds at the seaside course's signature 18th hole keeping balls wobbling and rolling out of position, Bhatia endured a hefty wait before missing a seven-foot birdie putt and closing with a par.
"Always nice to get off to a good start," Bhatia said. "Making six out of the first seven was pretty nice."
Despite his sizzling start, the 24-year-old American never made another birdie and finished 54 holes on 19-under 197, seeing a five-shot lead trimmed to two ahead of Sunday's final round.
"Just battling the elements at Pebble Beach is always fun," Bhatia said.
"Then you're holding on for a little bit once you get to eight, nine, 10, 12. And then 17 is a brutal hole today. Happy with today for sure."
Sharing second on 199 was two-time major winner Collin Morikawa, who birdied five of the last six holes to fire a 62, plus fellow American Jake Knapp and Austrian Sepp Straka. American Jacob Bridgeman was on 200 and Japan's Hideki Matsuyama on 201.
"I wanted to come out and win the tournament," Morikawa said. "Now we've given ourself a chance."
Bhatia, who shared third last week at Phoenix, seeks a third career PGA title after wins at the 2023 Barracuda Championship and 2024 Texas Open.
"One out of every 30 events we play can get this challenging," Bhatia said. "I'm just looking forward to that and having a good time."
Sunday's forecast features gusts around 35 mph after wobbling golf balls at 18 had Bhatia hoping for a moment for a delay to Sunday.
"I was hoping so but tomorrow doesn't look any better," Bhatia said. "Our golf balls were just oscillating and technically it's not a moving ball but it's just hard to get over a putt when you see your golf ball moving forwards, backwards, backwards, forwards. It's just brutal.
"It's hard to hit a putt like that with those conditions and with everything going on in your head. I was happy to make five there."
Bhatia began with birdie putts from five feet and nine feet on the first two holes, an eight-footer at the fourth and a 27-foot birdie putt at the par-three fifth.
His superb start ended with a six-foot birdie putt at the par-five sixth and a birdie putt from just inside eight feet at the par-three seventh.
Bhatia took bogeys at the par-three 12th and 17th holes.
Japan's Ryo Hisatsune, who had shared the 36-hole lead with Bhatia, stumbled to a 74 to stand on 203.
World number one Scottie Scheffler fired a 67 to share 22nd and stand eight adrift on 205, while defending champion Rory McIlroy fired a 72 to share 39th on 207.