Having already been overlooked by Bayern for striker Giovane Élber, the signing of striker Claudio Pizarro for the 2001–02 Bundesliga season would also limit his appearances, as Santa Cruz would regularly be substituted on to replace Pizarro or Élber. On 8 September, he scored his first goal of the 2001–02 season in round five, the second goal in a 2–0 away win to Borussia Dortmund. He played 79 minutes of the game before being substituted. On 23 October, he scored a brace in a 3–1 home win against Feyenoord during a 2001–02 Champions League group stage fixture as Bayern finished on top of Group H. He would be in the starting XI for the following two matches, where the second game saw him replaced after 42 minutes of the first half due to an injury. On 27 November, Bayern Munich defeated Boca Juniors 1–0 in the 2001 Intercontinental Cup, though he was not included in the squad. He returned to the first-team in a 5–1 away loss against Schalke 04 on 26 January, where he played the full 90 minutes. During the second group stage phase of the Champions League, he headed in a goal in the 81st minute from a Bixente Lizarazu cross in a 1–0 win against Boavista on 26 February. Bayern Munich were knocked out in the quarter-finals to Real Madrid as Santa Cruz made ten appearances in the competition. Santa Cruz finished the season with nine goals in 38 matches.