Gene J. Bertoncini was born April 6, 1937, in the Bronx to Italian immigrant parents: his father Mario played guitar and harmonica and ran a restaurant, and his mother Anita worked as a dressmaker. Music ran through the family; his older brother Renny performed on accordion and keyboards. Bertoncini started on guitar at age seven and was performing professionally by sixteen, appearing with Renny on NBC's The Children's Hour. His first real teacher was Johnny Smith, whom he met at NBC's studios, and he later studied classical guitar technique with Chuck Wayne.

He earned a Bachelor of Science in architectural engineering from the University of Notre Dame in 1959, playing clarinet in the marching band along the way, and worked briefly as an architect at David Henken's firm, a job that put him in the room for the design of Rudy Van Gelder's recording studio. After a stint in the Marines and a brief move to Chicago's jazz scene, where he worked with singer Carmen McRae, he settled permanently in New York and built a career as one of the city's most in-demand guitarists. From 1961 to 1962 he held the guitar chair in drummer Buddy Rich's working quintet alongside vibraphonist Mike Mainieri, an early professional partnership that continued informally for decades. He also spent time as a staff musician for ABC and NBC, including a run in the house band of the Tonight Show Starring Johnny Carson until the show's production moved to California in 1972, and he briefly toured with the Benny Goodman Sextet. In 1967 he performed with the Metropolitan Opera orchestra on classical guitar.

Bertoncini's first credited recording as a sideman was pianist Ahmad Jamal's Macanudo (1962), and by the end of that decade he was cutting sessions across pop and jazz alike, including guitar on Burt Bacharach's 1969 hit recording of "Raindrops Keep Fallin' on My Head." His signature sound emerged around 1970, after he heard recordings by the classical guitarist Julian Bream and began shifting his main instrument to nylon-string classical guitar just as bossa nova was reshaping American jazz repertoire. His first date as a leader, Evolution! (1969, Evolution Records), was a full studio-orchestra outing arranged around pop and jazz standards. That same period brought his most significant instrumental sideman credit: on August 26, 1970, he played guitar alongside vibraphonist David Friedman on Wayne Shorter's Odyssey of Iska (Blue Note, released 1971), a session also featuring Ron Carter and Cecil McBee on bass, Alphonse Mouzon and Billy Hart on drums, and produced by Duke Pearson.

Around 1970 Bertoncini met bassist Michael Moore, beginning a duo partnership he later called his "musical soulmate" collaboration; the two worked steadily through the 1970s and 1980s and reunited on record periodically for the rest of Bertoncini's life. Their duo albums, starting with Bridges (1977) and continuing through Close Ties (1984, an album of guitar-duo arrangements of Bach, Ellington, Gershwin and Ravel), O Grande Amor (1986, a bossa nova collection featuring Brazilian percussionist Edison Machado), Strollin' (1987) and Two in Time (1989), became the throughline of his recorded output and the clearest showcase of his classical-jazz crossover style. Alongside the duo records he worked as an accompanist to singers including Tony Bennett, Lena Horne, Nancy Wilson, Vic Damone and Eydie Gorme, and for eighteen years he held a solo residency at La Madeleine, a café in midtown Manhattan.

Bertoncini taught for roughly five decades, holding faculty positions at the Eastman School of Music, William Paterson University, New York University, the New England Conservatory, and the Banff School of Fine Arts in Alberta. His students included guitarists Peter Bernstein and Roni Ben-Hur, both of whom went on to their own recording careers. His musical relationship with Ben-Hur outlasted the classroom: the two guitarists co-led the duo album Smile (Motéma, 2008), the first release in the label's benefit series Jazz Therapy, and the following year they appeared together with fellow guitarists Bruce Arnold and Kenny Wessel on Master Guitar Symposium, Volume 2 (Mel Bay Publications, 2009), an instructional DVD filmed at NYU's Summer Guitar Intensive in 2006. Bertoncini's catalog through the 1990s and 2000s continued to lean toward guitar summits and duo projects: a trio date with bassist Rufus Reid and drummer Akira Tana on Acoustic Romance (1993), a session with pianist Bill Charlap and bassist Sean Smith (1998), duo albums with fellow guitarists Jack Wilkins, Frank Vignola and Royce Campbell, and the various-guitarists tribute We Remember Tal: A Tribute to Tal Farlow (1999), on which he appeared alongside Peter Bernstein, Mark Elf, Randy Johnston, Mundell Lowe and Jack Wilkins.

He continued performing into his late eighties, with regular engagements at Birdland and Mezzrow in his final years, and released his last studio album, Love Like Ours (Ambient Records, 2022), featuring Mike Mainieri on vibraphone. Bertoncini moved into the Lillian Booth Actors Home, an assisted-living facility in Englewood, New Jersey, in 2022 as age-related health issues made independent living difficult, and he kept performing there; he played a 45-minute set at the home on the day he passed away, August 29, 2026, of natural causes, at age 89. He never married and had no children; he was survived by his niece, Nina Collins, and his nephew, Paul Bertoncini.

Bertoncini was one of jazz guitar's foremost advocates for the nylon-string classical guitar, a sound he adopted after hearing the classical virtuoso Julian Bream and never abandoned, even when it meant turning down higher-profile work that called for an electric sound he considered wrong for the music, reportedly including an early offer to join Weather Report. His playing combined a light, singing touch with dense, carefully voiced chord-melody arrangements; colleagues and critics described his approach as "architectural," a nod to his engineering training, and Brazilian audiences and critics dubbed him "the Segovia of jazz guitar" for his ability to move fluidly between jazz standards, bossa nova repertoire, and classical pieces by Bach, Chopin and Ravel within a single set. His decades-long duo partnership with bassist Michael Moore became the definitive vehicle for that style, stripping the music down to two voices and letting his harmonic ideas carry the arrangements without a chordal safety net from piano or a second guitar.