Cardozo made his debut for Toluca in the 1995 season, but only appeared in three games, scoring no goals. However, in the subsequent winter season, he scored 7 goals in 13 games. In his eight years with the team, he has scored a record 249 goals for the club, including 14 in the 2004 Apertura. On 24 April 2005, he moved to the 4th spot in the list of all-time top scorers in the Mexico Primera Division after Jared Borgetti scored his 250th goal with Monarcas Morelia.
Due to his work at Toluca, Cardozo was elected as the Paraguayan Footballer of the Year in the years 2000, 2002 and 2003; and the South American Footballer of the Year in 2002. Despite the fact that he was fiercely opposed to the move, Cardozo was transferred to Argentine team San Lorenzo de Almagro in June 2005, and finished the season with only 4 goals due to injuries that kept him away from playing several games. However, many critics lambasted Cardozo for refusing to play through the pain. While playing for Toluca, Cardozo struggled through the 1997 campaign with hamstring problems and then played through much of the 2001 season despite suffering a broken wrist in the season opener. Cardozo is the all-time leading scorer for Club Toluca.
Cardozo, also owns the title of highest scorer in just one season, in the Apertura 2002 he scored a total of 29 goals, becoming the maximum goal scorer in Mexican's football league that year.
In July 2006, Cardozo attempted to return to Club Olimpia to finish his career. He was unable to re-sign for the club because the Paraguayan league's transfer deadline had already passed. As a result of his inability to sign for Olimpia, he decided to retire from football. He scored 342 goals total in his career. In June 2008 a farewell match was organized in the city of Toluca to honor his career and contributions to football. Cardozo scored two goals in the match which had a sellout crowd.
In November 2006, Club Olimpia's coach Oscar Paulin was fired due to poor performances by the team and Cardozo was named as the interim coach of the Paraguayan club, this being his first experience as a coach. He coached for the remainder of the year and for the 2007 Apertura tournament.
In October 2009 he was hired to be an assistant coach for the team of Indios de Juarez for the Apertura 2009.
Cardozo returned to Olimpia Asunción in November 2009 following coach Carlos Kiese's resignation.
In 2011, he was hired as coach Querétaro FC where he led the team into their first liguilla and the team's all team highest place (8th) and points (26) in Primera División regular season. He managed to eliminate Guadalajara in the Quarter Finals and advance to a surprising semi-final where they lost to champions Tigres UANL 1-0. The following season however, Querétaro began the season with poor results, which once again emerged relegation problems against rivals Atlas and Estudiantes Tecos (relegated) which led to Cardozo's resignation.
After spending the 2011 and 2012 seasons at Querétaro, he was appointed to manage Olimpia once again on September 25, 2012 after the departure of Gregorio Perez.
On May 7, 2013, Cardozo was announced as the new manager/technical director for Club Deportivo Toluca of Mexico where he played for 10 years (1995-2005).