The agency says its agents tracked and stopped a Kia Forte in Escondido on Tuesday and found nearly $34,000 stashed in the car's center console.
Authorities say another car sped off as the first vehicle was stopped but it was later found abandoned nearby.
That car, a Volkswagen Passat, had more than $3 million packed in boxes in the trunk.
The driver was found hiding in some brush.
Both men - one a U.S. citizen and the other from Mexico - were arrested on suspicion of currency smuggling.