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. 2002–03 season Santa Cruz made his first appearance of the 2002–03 season on matchday 9 in a 1–0 away win against Hansa Rostock, where he was substituted on to the field for Claudio Pizarro in the 76th minute. The striker scored his first goal of the 2002–03 Champions League in a 2–1 loss against Deportivo La Coruna on 29 October; he was substituted onto the field for Hasan Salihamidžić in the 46th minute and scored in the 77th minute. Bayern, however, finished bottom of their group with just two points. His first goal of the 2002–03 season came in a 2–1 home win against Borussia Dortmund on 9 November. One week later, he scored the only goal in a 1–0 win against VfL Wolfsburg on 16 November. In the following match, he scored Bayern Munich's second goal in a 2–0 win against 1. FC Kaiserslautern on 23 November. This was the first time that he had scored a goal in three consecutive games for Bayern Munich. Two weeks later, he scored a brace in a 3–0 away victory to VfB Stuttgart on 7 December. Due to injury, the Paraguayan was reduced to only 14 league appearances for the 2002–03 season as Bayern Munich finished on top of the 2002–03 Bundesliga table with 75 points. Bayern Munich defeated 1. FC Kaiserslautern 3–1 to claim the 2002–03 DFB-Pokal on 31 May, Santa Cruz was not included in the squad. Santa Cruz finished the season with eight goals in 19 matches.