Zeballos started his career in the youth divisions of Sol de América where he played alongside José Ortigoza. He made his debut in 2005 and helped the team to win the Paraguayan División Intermedia tournament by being the team's top-scorer. He is remembered for his goal against Club Cerro Corá at the last minute of the match.
His good form rewarded him with a transfer to Cruz Azul of Mexico. He debuted against San Luis F.C. in the Jornada 3 of the Clausura 2008, making his first goal in the Primera División de México one minute after being substituted in for Nicolás Vigneri. In the liguilla del futbol Mexicano he brought the team back up to beat Jaguares in quarter-finals and took them all the way to the final where they would lose. On 15 November 2008, Zeballos scored his first "hat-trick" with Cruz Azul against Jaguares.
In January 2010, Zeballos was loaned to Primera División Paraguaya club Cerro Porteño until 31 December 2010. With Cerro Porteño he won two second places and was top scorer of the Torneo Apertura with 16 goals along with Rodrigo Teixeira, and ended up being top scorer of the year with 24. On 12 December 2010, it was reported that former club Oriente Petrolero and various clubs from Bolivia's Liga de Fútbol Profesional had shown there interest in Zeballos.
At the end of that year, Zeballos signed a contract with rival of Cerro Porteno, Olimpia. Olimpia came up second during the Torneo Apertura 2011 with him as top scorer having scored 13 goals. On the next tournament of the year, Zeballos managed to win the Torneo Clausura with Olimpia, being the team's top scorer with 12 goals, one behind the tournament's top scorer Fredy Bareiro. With this record, Zeballos was top scorer of the 2011 season in Paraguay with a total of 25 goals, attracted on themselves the attention of Genoa and Cagliari.
He arrived to the Emelec, where he was loaned for a great sum of money, but only managed one goal during his time, for which he was criticized by the fans and the media that he wasn't worth the amount paid for. He left Emelec after just appearing in 17 games. Zeballos left Emelec to join Kyrlia again but this time with no success after long and exhausting negotiations during summer 2014 Zeballos returned to Club Olimpia, but by judicial problems he couldn't sign a contract and then started negotiations with Botafogo.
Botafogo
After a lot of negotiation Zeballos arrived at Rio de Janeiro to sign with Botafogo. He scored his first goal, of penalty, in a match of the Cariocão 2014 against Boavista.
Libertad
During December 2015, it had already been reported that Zeballos had a %99 chance of departing Olimpia. By 7 January 2016, it was announced that Zeballos had joined Club Libertad and the following day he had travelled to the city ofMinga Guazú to join the club in their pre-season training.
