Raul Villarreal and his brother, Fidel, were also convicted of accepting bribes and conspiring to launder money.
Before the case, Raul Villarreal often appeared as a high-profile spokesman for the US Border Patrol agency.
An investigation into the men was launched in 2005 following a tip-off.
A third man, Armando Garcia, was also found guilty of charges similar to those faced by the two brothers.
The court heard that on several occasions in 2005 and 2006, Garcia led groups of Mexican and Brazilian immigrants across the border on foot to be then picked up by the Villarreal brothers in their patrol vehicles and released in the US, according to media reports.
The prosecution case was based on evidence gathered from surveillance cameras installed at pick-up points, GPS devices installed in patrol cars, footage from an aircraft used to track a smuggling run, as well as witnesses accounts.
One Brazilian women testified that she paid $12,000 (£7,600) to cross the border.
“They made the border work for them,” prosecutor Timothy Salel told jurors, the San Diego Union-Tribune daily reports.
In 2006, the two men were themselves tipped off about the probe and fled to Mexico, where they settled in the city of Tijuana, across border from San Diego.
They were arrested by Mexican police and extradited to face trial in the US in 2008.
The brothers, who will be sentenced in November, face a maximum of 50 years in prison and fines of at least $1.25m (£800m), according to the Associated Press news agency.
A second accomplice, Claudia Gonzalez, pleaded guilty in December 2009 and will be sentenced in September.
BBC © 2012