Jonathan Santana

Santana's debut was in the 1998–99 season in Argentina's lower leagues, appearing in the squad with Japanese defender Shinji Muraki. He went on to play for a number of Argentine Primera clubs, including San Lorenzo and River Plate.

San Lorenzo

For the 2001–02 season, Santana joined San Lorenzo de Almagro for the 2002 Copa Libertadores and Copa Sudamericana tournaments, winning the latter and forming the squad with Cameroon midfielder William Tabi. In the 2004–05 season, Santana appeared for San Lorenzo in the Copa Libertadores in the squad with Ezequiel Lavezzi.

River Plate

For the 2005–06 season, Santana joined Argentine River Plate, reaching the quarter-final stages of the Copa Libertadores. Santana formed part of a high-profile team that included Juan Pablo Carrizo, German Lux, Diego Buonanotte, Marcelo Gallardo, Daniel Montenegro, Oscar Ahumada, Matias Abelairas, Luciano Figueroa, Gaston Fernandez, Gonzalo Higuaín, Colombian striker Radamel Falcao and future Paraguay national team colleague Julio Cesar Caceres.

Wolfsburg

In August 2006, he signed a five-year contract with German VfL Wolfsburg. Whilst Santana was at Wolfsburg during the 2006–07 season, he formed part of the team with Paraguayan Julio dos Santos. For his second season at the club, Santana was teammates with Edin Dzeko.

San Lorenzo (loan)

During a loan move to San Lorenzo in the 2008–09 Argentine Primera División season, he joined Paraguayan Aureliano Torres in the…

In June 2007, Santana received Paraguayan citizenship (his mother is a Paraguayan citizen born in San Ignacio, Misiones Department and Argentina did not recognize dual citizenship). He played for Paraguay in the 2007 Copa América. He was also named in Paraguay's final 23-men squad for the 2010 FIFA World Cup. He entered the field during Paraguay's first game, a 1–1 draw with Italy, but suffered an injury during the match. However, as Paraguay's coach Gerardo Martino had already made the three available substitutions, Santana had to stay on the field and play injured for the remaining time.

Following his retirement from football in 2021, Santana and his wife modelled for a clothes store at Asunción shopping centre Paseo la Galeria.

San Lorenzo

Copa Mercosur: 2001 VfL Wolfsburg

Bundesliga: 2008–09