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.
Prosecutors say that before the discovery, officers saw several vehicles come and go from the property in Tijuana and the warehouse on Friday 13 May.
They were then stopped and searched, the drugs were seized and arrests were made.
When officers entered the warehouse, the cross-border tunnel exit point was found carved out of the floor.
The attorney's office said 1,762lb (799kg) of cocaine, 164lb (74kg) of methamphetamine and 3.5lb (1.5kg) of heroin had been seized.
The suspects, aged between 31 and 55, could face a life sentence in prison and a $1m fine if found guilty.
"There is no more light at the end of this narco-tunnel," said US Attorney Randy Grossman.
"We will take down every subterranean smuggling route we find to keep illicit drugs from reaching our streets and destroying our families and communities."
The last tunnel found in California was in 2020. That one is also the longest to date, measuring 4,309ft (1,313m) in length. Since 1993, 90 of these types of secret passage have been discovered.