On 10 February 1999, at age 22, the Italian under-21 international was rewarded by the coach of the senior team, Dino Zoff, for his displays. He earned his first cap in a 0–0 friendly against Norway in Pisa, Italy. He became the first player of Bari to play for the national side in 50 years. Throughout the 1998–99 season, he made 32 appearances and scored four goals. Halfway through this season, he was brought to Juventus, by Carlo Ancelotti for reported 30 billion Italian lire (€15,493,707, but 3 billion lire paid via Simone Perrotta's 50% rights) and would play in the black-and-white jersey starting the season after.
After the transfer to Juventus on 1 July 1999, Zambrotta continued his upward momentum under manager Carlo Ancelotti. He made 32 league appearances with one goal in the first season he played for Juventus. On 14 May 2000, the last match day of the season, Juventus missed out on the 1999–2000 Scudetto, as they were defeated 1–0 away at Perugia in the heavy rain, while Lazio got the three points at home by beating Reggina 3–0, and overcame Juventus by a single point. Zambrotta was brought on in the second half in that game and was later given a red card by the referee, Pierluigi Collina. In his second season for Juventus, 2000–01, Zambrotta made 29 league appearances and scored three goals, but Juventus finished once again in second place in Serie A, behind Roma. Zambrotta won his first Scudetto in the 2001–02 season, while he made 32 league appearances and scored one goal during the season, also reaching the 2002 Coppa Italia Final with the club. After Zambrotta suffered an injury in the game against South Korea during the 2002 World Cup, he missed the beginning of the 2002–03 Serie A campaign. During his absence, the new signing of Mauro Camoranesi took his place on the right wing and was in superb form. This prompted then coach, Marcello Lippi, to switch Zambrotta to the left-back when he returned to action. Zambrotta adapted to his new position very quickly and performed particularly well, demonstrating his pace, stamina, work-rate, technical ability, his tactical intelligence and versatility, as well as his ability to contribute both offensively and defensively.
It was on tour with the under-21 team that Zambrotta earned the nickname "the Mermaid" for his allegedly spending one hour every night in front of the mirror grooming at his now trademark goatee. After some impressive displays for the U21 and an excellent start to the 1998–99 season, Zambrotta earned his first senior cap on 10 February 1999, nine days before his 22nd birthday, in an 0–0 friendly draw with Norway.