With a length of 1,744ft (531m), the passage had a rail track, electricity and a ventilation system.
US authorities had been carrying out surveillance at a property previously used as a stash house for smuggling cocaine when they made the discovery.
They seized cocaine, methamphetamine and heroin. Six people are being held on drug-trafficking charges.
The US Attorney's Office for the Southern District of California said the tunnel was 61ft (18m) deep and 4ft (1m) in diameter.