He was scouted by U.S. Lecce sports director Pantaleo Corvino and signed in the summer of 2001. Despite his 12 goals in 27 games, Lecce were relegated that season into Serie B and Chevantón stayed with them. His presence would prove vital, scoring 18 goals in 30 games to promote Lecce straight back into top flight domestic football. In the Serie A 2003-04 he was the fourth goalscorer of the tournament with 19 goals and became the all-time goalscorer for Lecce, overcoming former Argentinian national team and Lecce player Pedro Pablo Pasculli.
Following the loss of Fernando Morientes (returning to Real Madrid after his loan period expired), Didier Deschamps was looking to reinforce his frontguard and so made an offer for Chevantón. In July 2004, he transferred from Lecce in Italy to A.S. Monaco on a free transfer. Unfortunately, he wouldn't hit the form he had in the Italian leagues, hampered by knee injuries in the first season. After sparse appearances in his first season, transfer speculation was growing after his future at the club seemed in doubt. However, after returning from a knee operation in March 2005, fans were treated to a glimpse of the talent Javier holds, scoring in every game he played in thereafter.
The beginning of Chevantón's season at Sevilla started with a back strain which put him out for the first few weeks, but he scored four goals for Sevilla in the UEFA cup against SC Braga, AZ Alkmaar, Shakhtar Donetsk and Grasshopper-Club Zürich, and scored his first La Liga goal by way of a stylish bicycle kick at home against Real Madrid on December 9, 2006, which lead to the home team's 2-1 victory. The second time Sevilla met Real Madrid that season Chevantón scored another goal with an excellent free kick. He recently netted the equaliser against Arsenal in a pre-season friendly for Sevilla in a 1-1 disappointment at the Emirates but has since found opportunities in the Spanish League limited.
On 26 November, 2009, he was given permission to trial with Serie A club Atalanta, who ultimately agreed a loan deal with Sevilla. The player joined the club on January 2, 2010, until the end of the 2009-10 season.
Run-ins with the Uruguay assistant coach have restricted his playing time for the national team, most strikingly obvious was his omission from the 2006 world cup qualification squad. Uruguay failed to qualify for the 2006 World Cup. After a long spell out of the national side Chevanton was finally included back in the Uruguay national squad for world cup 2010 qualifers on the 27th of September 2008. The qualifers were against Argentina and Bolivia.