The news was confirmed by a post on Becker's personal website.
The cause of death has not been announced yet.
According to Variety, Becker had recently cancelled his appearances at the Classic West and Classic East concerts due to illness.
His band member Donald Fagen released a statement describing their long partnership and said, "I intend to keep the music we created together alive as long as I can with the Steely Dan band."
Born on February 20, 1950, Becker was raised in the borough community of Queens, New York. He was a saxophonist initially, but took up the guitar in his teenage.
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He withdrew from his college without a diploma and after Fagen graduated in 1969, they moved to Brooklyn to pursue a career in music.
The duo served as studio members of the pop act Jay and the Americans. In 1971, they decamped to Los Angeles to serve as house songwriters for ABC/Dunhill, the publishing firm operated by the Americans' record label.
Their songwriting impressed label president Jay Lasker, who offered the pair a contract. They organised a working group with New York guitarist Denny Dias, guitarist Jeff "Skunk" Baxter and drummer Jimmy Hodder.
The track "Do it again" from the album went on to become a massive hit on the radio, followed by the single "Reeling in the years".
Steely Dan's sophomore set 'Countdown to Ecstasy' (1973) included "My old school," a backhanded tribute to Fagen and Becker's alma mater Bard - was perhaps too bitter for most listeners and failed to strike a chord with the listeners.
A confluence of difficulties led to the band's dissolution in 1981.
Becker, then retreated to the Hawaiian island of Maui, where he battled drug abuse and stayed away from the public glare.
He came back as a producer and directed albums by China Crisis ('Flaunt the Imperfection,' 1985), Rickie Lee Jones ('Flying Cowboys,' 1989) and Michael Franks ('Blue Pacific,' 1990).
Becker's first work after his break-up with Fagen was Rosie Vela's 1986 collection 'Zazu'.
Their 2000 album 'Two Against Nature' collected four Grammys, including one for album of the year.
Becker also undertook solo recording after his reunion with Fagen - albums '11 Tracks of Whack' (produced by Fagen in 1994) and 'Circus Money' (2008), which failed to duplicate the group's success.
He was inducted into the Rock and Roll Hall of Fame with Fagen in 2001.