The guitarist, raised in Germantown, was introduced to music at Providence Baptist Church, founded by his grandfather, Rowland C. Lamb Sr.
Mr. Johnson, who graduated from Central High School, earned a reputation as a musician's musician during a career of more than three decades, beginning in the '70s, when he was a teenager playing on gospel recordings by the Rev. James Cleveland.
Before the decade was out, Mr. Johnson was filling in for Carlos Santana in jazz piano giant McCoy Tyner's road band. In the 1980s, Mr. Johnson's collaborators included the smooth-jazz chanteuse Phyllis Hyman and the avant-jazz drummer Ronald Shannon Jackson.
He made his first recordings with Philadelphia violinist John Blake in 1985, and was briefly a member of Paul Schaffer's "World's Most Dangerous Band" on Late Night With David Letterman. As a studio guitarist, he worked with George Duke, Jeff Beck, Roberta Flack, Stanley Clarke, Erykah Badu, and, most recently, the jazz crossover star Esperanza Spalding.
In 1996, he released Blue, the first of a series of solo albums that could move from quietly luminous acoustic interludes to noise-rock freakouts.
In 2008, Mr. Johnson played on Rediscovering Lonnie Johnson, a tribute to the blues and jazz guitar great who died in 1970. In an Inquirer interview about that project, Mr. Johnson's words could aptly have described his own music.
"There was some fiery music," he said. "There was jazz, there was blues. He was playing everything at once. I guess he was dying to get it out."
As a guitarist, "Jef was instantly identifiable," said Aaron Luis Levinson, the Grammy-winning producer who played with Mr. Johnson in the jazz-noise band Gutbucket and chose him to "play" Lonnie Johnson on the Rediscovering album.
Levinson raved about Mr. Johnson's "pentatonic funky simplicity mated with an avant-gardist's sense of searching and a jazz cat's manual dexterity." Mr. Johnson, he said, "was literally unlike anyone else that ever played the guitar."
Mr. Johnson's fellow musicians were quick to praise him as word of his death spread.
The Roots drummer Ahmir "?uestlove" Thompson, who played with Mr. Johnson in the Soulquarians, who backed up D'Angelo in 1990, as well as on the Roots' 2002 album Phrenology, wrote on Facebook that Mr. Johnson's "axe game was BAR NONE. . .. The proudest night of my life was watching Prince sit jaw-dropped as we finalized JLJ's guitar solo on the highly underrated 'Jimi Was a Rock Star' " (on Common's 2002 album Electric Circus).
James Poyser, record producer and keyboard player for the Roots, was similarly effusive, calling Mr. Johnson on Facebook "one of the world's greatest guitar players and one of my favorite human beings, a real friend and mentor."
Levinson said a scholarship fund was being set up in Mr. Johnson's name at the Germantown branch of Settlement Music School.
In addition to his brother, Mr. Johnson is survived by three sisters. His wife, Trisha, died in 2001.
A memorial service is planned.
Contact Dan DeLuca at 215-854-5628 or email@example.com or on Twitter: @delucadan.