The half-mile passage runs from a residence in Tijuana to a warehouse in San Diego's Otay Mesa area, the San Diego Tunnel Task Force said in a statement.
Investigators suspect a major drug cartel was the driving force behind two long, sophisticated tunnels connecting Mexico with the U.S. that were discovered this month along with more than 40 tons of marijuana.
Authorities said an underground passage located Thursday was similar to one found earlier -- both running around 2,000 feet from Mexico to San Diego and equipped with lighting, ventilation, and a rail system for drugs to be carried on a small cart.
The tunnels are believed to be the work of Mexico's Sinaloa cartel, headed by that country's most-wanted drug lord, Joaquin "El Chapo" Guzman, said Mike Unzueta, head of investigations at U.S. Immigration and Customs Enforcement in San Diego.
"We think ultimately they are controlled by the same overall cartel but that the tunnels were being managed and run independently by different cells operating within the same organization," Unzueta said Friday.
The tunnel found Thursday is more than seven football fields in length and extends from the kitchen of a home in Tijuana, Mexico, to two warehouses in San Diego's Otay Mesa industrial district.
Three men were arrested in the United States, and the Mexican military raided a ranch in Mexico and made five arrests in connection with the tunnel, authorities said.
U.S. authorities have discovered more than 125 clandestine tunnels along the Mexican border since the early 1990s, though many were crude and incomplete.
The passage found Thursday is one of the most sophisticated to date, with an entry shaft in Mexico lined with cinderblocks and the rail system, Unzueta said.
U.S. authorities do not know how long the latest tunnel was operating. Unzueta said investigators began to look into it in June on a tip that emerged from a large bust of marijuana, cocaine and methampethamine by the San Bernardino County Sheriff's Department.
U.S. authorities followed a trailer from one of the warehouses to a Border Patrol checkpoint in Temecula, where they seized 27,600 pounds of marijuana. The driver, whose name was not released, was arrested, along with two others who went to a residence in suburban El Cajon that had $13,500 cash inside.
"That (trailer) was literally filled top to bottom, front to back," Unzueta said. "There wasn't any room for anything else in that tractor-trailer but air.
"Three tons of marijuana were found in a "subterranean room" and elsewhere in the tunnel on the U.S. side, authorities said.
Mexican officials seized four tons of pot at a ranch in northern Mexico, bringing the total haul to more than 20 tons.
The discovery of the cross-border tunnel earlier this month marked one of the largest marijuana seizures in the United States, with agents confiscating 20 tons of marijuana they said was smuggled through the underground passage. That tunnel ran the length of six football fields under the border and warehouses in Mexico and San Diego. One of the warehouses involved in the tunnel discovered Thursday is only a half-block away.
In Thursday's discovery, the tunnel's cinderblock-lined entry in Mexico dropped 80 to 90 feet to a wood-lined floor, Unzueta said. From the U.S. side, there was a stairway leading to a room about 50 feet underground that was full of marijuana.
"It's a lot like how the ancient Egyptians buried the kings and queens," Unzueta said.
Several sophisticated tunnels have ended in San Diego warehouses. ICE began meeting with landowners last month to warn them about leasing space to tunnel builders.
"These owners of warehouses, they need to know their customers, they need to know who's in there leasing these things," Unzueta said.