Webber was born on 27 August 1976 in Queanbeyan, New South Wales, Australia. He began karting at around twelve or thirteen and progressed through Australian Formula Ford before moving to Europe in late 1995. After strong seasons in European and British Formula Ford in 1996, he competed in the British Formula Three Championship with Alan Docking Racing in 1997, finishing fourth overall, winning the Brands Hatch Grand Prix event, and being voted Rookie of the Year. Rather than continue in British F3, Webber accepted an opportunity to race for the AMG Mercedes team in the FIA GT Championship in 1998, pairing with Bernd Schneider. He and Schneider won five races, finished championship runner-up, and competed at Le Mans — an experience that broadened his technical understanding significantly before he turned to single-seater racing in Formula 3000.
Webber's Formula 3000 debut came in 1999 with the European Aviation team, which was connected to Paul Stoddart's motorsport activities. He finished third in the Drivers' Championship with 21 points, winning at Silverstone and achieving two further podium results despite four retirements. The season also included F1 testing activity and a troubled appearance at Le Mans in the Mercedes CLR — a car aerodynamically compromised enough to become airborne twice, forcing his withdrawal. In 2000, Webber continued in F3000 at a lower level, finishing outside the top positions overall.
For 2001, Webber joined Super Nova Racing, the reigning teams' champions and the outfit that had previously fielded Juan Pablo Montoya for his 1998 championship-winning season. Webber entered the season as a title favourite. He won at Imola, Monaco, and Magny-Cours and finished second at the Nürburgring, building a championship position that should have been unassailable. However, four consecutive retirements in the final four rounds of the season — a run of mechanical and on-track failures that prevented him from scoring in the decisive stages — cost him the title. He finished with 39 points, runner-up to Justin Wilson by a margin that reflected misfortune rather than a deficit in pace or car management.
Despite the disappointment of the 2001 F3000 campaign, Webber's F1 testing work — initially with Benetton and then ongoing — had established him as a candidate for a Grand Prix seat. Ron Walker and telecommunications company Telstra successfully lobbied for Webber to take a Minardi drive for the opening rounds of the 2002 Formula One season, replacing Fernando Alonso. Paul Stoddart retained him for the remainder of the year after Webber finished fifth on his debut at the Australian Grand Prix. His F3000 runner-up finish, combined with his sports car experience and testing record, made the case that he was ready for the transition even without a championship to his name.
Webber's Formula 3000 career is remembered primarily for the 2001 near-miss — a title that was statistically within reach and lost to retirements rather than outright pace. His broader junior and sports car portfolio was unusual for a future Formula One driver of his era: the FIA GT stint with Mercedes gave him technical and endurance experience that most contemporary F3000 graduates lacked. He would go on to win nine Formula One Grands Prix with Red Bull Racing, finish third in the World Drivers' Championship in 2010, 2011, and 2013, and win the FIA World Endurance Championship with Porsche in 2015.