Officials have arrested eight people and seized more than 20 tons of marijuana.
The tunnel had two U.S. entrances located in warehouses about 800 feet apart. The tunnel was equipped with advanced rail, electrical and ventilation systems.
The house in Tijuana had a garage that was big enough to accommodate deliveries by tractor trailer trucks.
Federal agents discovered the tunnel as a result of an ongoing investigation. Officials who were conducting surveillance in the Otay Mesa area saw suspicious activity involving a tractor trailer truck parked at a warehouse located in the 10000 block of Marconi Drive.
Agents continued to monitor the truck after it left and alerted border patrol officers. When the truck's trailer was searched at the checkpoint in Temecula, 27,600 pounds of marijuana was found.
The driver was arrested and faces federal drug-smuggling charges.
"This discovery again shows the cartels' growing desperation in the face of beefed up border security and the costly extremes these organizations are trying in an effort to avoid detection," said Miguel Unzueta, special agent in charge for ICE Homeland Security Investigations in San Diego.
Officials said the investigation is ongoing.
Earlier in November, another tunnel was discovered and more than 20 tons of pot was confiscated.
The Associated Press contributed to this report.