The hard-hitting Californian was in a hole at 3-0, 40-0 down in the first set but rallied to break back and ultimately force a tiebreak he won to the delight of the partisan crowd.
Berrettini came out in full force to win the second set but Querrey's blistering serve, highlighted by an unreturnable second serve on match point, eventually proved too much for the Italian.
"It was windy all day, which made things tough. It was one of those matches I'm happy to just kind of get through it," Querrey said in an interview after the match.
Next up for Querrey on Saturday is a re-match with 13th seed Milos Raonic, who won their Indian Wells quarter-final contest a year ago.
News that makes sense
Your trusted source for staying up-to-date with the world around you. Get free daily news updates and analysis, straight to your inbox.
Querrey, who plays a similar style to the big-serving Canadian, said the key would be taking advantage of rare break point opportunities.
"When you play a guy like him you hopefully get a couple of break points during a match and you have to come out on top of those," he said.
"Last year he did a better job of winning those big points."
Another Californian, qualifier Marcos Giron, also won his first-round match with victories in two tiebreakers seeing off Frenchman Jeremy Chardy 7-6(3) 7-6(1).
Giron, who needed a wild card just to get into the qualifiers, will next face Australian Alex de Minaur, the 23rd seed.
German Jan-Lennard Struff thumped six aces to send Australian John Millman packing 6-1 6-3 in their evening clash.
Other first-round winners on Thursday included Japan's Yoshihito Nishioka, German Philipp Kohlschreiber, Slovak Martin Klizan and 18-year-old Canadian Felix Auger Aliassime.
Earlier in the day, Grigor Dimitrov withdrew from the tournament with a shoulder injury.
The Bulgarian has not played since the Australian Open and will look to return to the court at next month's Miami Open.
(Reporting by Rory Carroll, editing by Nick Mulvenney and Sudipto Ganguly)
