The singer was found unresponsive at lunchtime on Saturday, St Charles County police said.
Berry's seven-decade career boasted a string of hits, including classics Roll Over Beethoven and Johnny B. Goode.
He received a lifetime achievement Grammy in 1984 and was among the first inductees to the Rock and Roll Hall of Fame in 1986.
In a statement on Facebook, the St Charles County Police Department said they were called to reports of an unresponsive man at 12:40 local time (17:40 GMT).
"Unfortunately, the 90-year-old man could not be revived and was pronounced deceased at 1:26pm," the statement continued.
"The St. Charles County Police Department sadly confirms the death of Charles Edward Anderson Berry Sr., better known as legendary musician Chuck Berry."
Motown legends The Jacksons paid tribute.
"Chuck Berry merged blues & swing into the phenomenon of early rock'n'roll. In music, he cast one of the longest shadows. Thank You Chuck," they tweeted.
Berry was born in St Louis, Missouri, in 1926, and had his first hit Maybellene in 1955.
Last year, he announced he would be releasing his first album in nearly four decades. He dedicated it to his wife of 68 years, Themetta "Toddy".