Cáceres' first club was Primera División de Paraguay club, Olimpia, where he helped the club become Paraguayan champions twice. In 1999, after winning the Apertura tournament, and finishing third in the Clausura tournament they were crowned champions with a 4–2 aggregate win over Cerro Porteño in the National championship game. In 2000 they again won the Apertura tournament, and also won the Calusura tournament, thus were crowned champions. He was also part of the team that won the Copa Libertadores in 2002 as well as the Recopa Sudamericana in 2003. He made a total of 84 league appearances in four years at the club, scoring five goals.
In 2004, he signed for French Ligue 1 club Nantes. He made his league debut on 14 August 2004 in a 1–1 draw with Bastia. However, he later suffered an injury and did not play for several months. By the time he had recovered, Nantes had a new coach who did not play Cáceres and he was loaned to BrazilianBrasileirão club Atlético Mineiro for the 2005 season. His league debut came on 11 September 2005, a 2–0 defeat to Botafogo. He made fourteen league appearances, scoring two goals. However, the club finished in 20th place and were relegated to Brasileiro Série B. In January 2006, he moved to Argentina, signing for River Plateon loan, where he quickly became a key player and squad captain. He made his league debut in a 5–0 win at Tiro Federal on 29 January. He was also a part of the River Plate team that reached the quarter-finals of the 2006 Copa Libertadores. Later in 2006 he spent two months in Spain, from October to December, with Catalan club Gimnàstic de Tarragona in La Liga where he made eleven league appearances.
In January 2007 Cáceres moved to Mexico when he was signed by Tigres, with whom he maintained a regular starting position. He made his league debut in a 2–1 defeat at Tecos on 20 January 2007 and scored his first goal for the club on 3 March in a 3–2 win over Chiapas. He made a total of 32 league appearances, scoring two goals.
In January 2008 he moved again to Argentina, signing for Boca Juniors. He made his league debut on 10 February 2008 in a 1–1 draw with Rosario Central. On 14 May he scored Boca's first goal as they were held to a 2–2 home draw by Mexican club Atlas in the quarter-finals of the 2008 Copa Libertadores In October 2008 Cáceres had a very public conflict with Boca teammate Juan Román Riquelme, when in an interview on a Paraguayan radio station in Asunción, where he was training with his national team, Cáceres questioned Riquelme's motivation. He claimed that "In some matches, he is apparently running and in others he is passive. He seems to be mentally saturated. He seems to have more motivation when he plays for his country." However, Riquelme responded in a telephone interview on the Fox Sports cable channel, saying "He doesn't know what I feel for the club. I take part in pre-match concentration just like the other players and I didn't have a holiday because I chose to play in the Games. When we won the gold, I ran to the airport so I could play in the final." And adding, "These things should be kept in the dressing-room, he's broken all the codes of football." However, after Boca won the Superclásicoderby match over Buenos Aires rivals River Plate 1–0 at El Monumental on 21 October 2008, Cáceres said that the conflict "has been left behind", adding that the relationship between the two players had improved. Caceres scored his first goal for Boca Juniors in a 2–1 win against Lanus 30 August 2009.
