"I have been doing a lot of endurance and speed work ... so I was really confident in what I could do," said Lyles, one of America's top young sprinters.
Berry unleashed a toss of 25.60 metres on her final throw, bettering the previous best of 25.56m by American Brittany Riley in 2007.
"I really injured [my back] four weeks ago, and two weeks ago I wasn't even going to come but I fought it out," said Berry.
World records are not recognised in the two events because they are held so infrequently.
Lyles, the 2016 world under 20 100m gold medallist, narrowly missed making last year's Olympic team as he finished fourth in the 200 at the American trials.
Runner-up Paul Dedewo also dipped under 32 seconds, finishing in 31.92 seconds, the third-fastest time ever indoors.
Berry, a hammer thrower outdoors, last summer was stripped of her pending American record in that event and suspended by the U.S. Anti-Doping Agency for three months for using a prohibited medication.
Olympic medallists Paul Chelimo and Sam Kendricks also were winners.
Chelimo, who grabbed the silver medal in the 5,000 metres at last summer's Rio Olympics, ran away with the men's two mile. His time of eight minutes, 28.53 seconds was more than 10 seconds faster than second place finisher Woody Kincaid.
Kendricks, the Olympic bronze medallist, dominated the pole vault with a clearance of 5.85 metres.
The championships conclude on Sunday.
(Reporting by Gene Cherry in Salvo, North Carolina; Editing by Andrew Both)
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