Early in his career, Vera played for several Paraguayan clubs such as Resistencia, Sol de América and Sportivo Iteño before moving to Ecuador where he played for teams like Aucas, Olmedo, and LDU Quito. At the end of 2007, he was named best foreign player and best overall player of the Ecuadorian league by the newspaper El Comercio.
During the 2008, Vera was important member of the LDU Quito squad that won the 2008 Copa Libertadores, the first international for the club and for any club in Ecuador. Vera was nominated in the ideal team of the cup when he was chosen as an ideal substitute in the midfield position, along with teammates Damián Manso and Joffre Guerrón. Shortly after the Copa Libertadores win, he signed a 4-year contract to play for Mexico's Club América. Vera scored his first goal for the Mexican side in his 4th game with the team in the Apertura 2008 1–1 draw against Pachuca. On 18 June 2009, Vera was loaned back to LDU Quito after a bad spell at América. In the short time back, he was a key player for the club as they won two more international titles: the 2009 Recopa Sudamericana and the 2009 Copa Sudamericana. He was sold to Atlas by America before the 2010 World Cup, where he would play with Paraguay. After a rather uneventful stint at Atlas, he returned to Ecuador for his third stint at LDU Quito. He has publicly stated he would like to retire at the Quito-based club. Enrique Vera in 2011 during his game with Liga de Quito he left with a broken leg that took him out for more than a year until he returns to the field. In 2012 he was getting back into shape to started his new season with Liga de Quito in 2013 season