The Bayshore Cut-off was completed December 8, 1907. The new line shortened the distance between San Bruno and San Francisco by four miles and eliminated Bernal Cut as a mainline. The original line through Bernal Cut remained as a branch line with one passenger train a day which operated until 1930. The last through-freight train operated over the old line in 1942, after which the middle section was abandoned, leaving the line between San Bruno and Daly City on the south  end and a section within Yard Limits from San Francisco to Flktm

Today (in 1998) only a 3.3-mile section from South San Francisco to the end of the branch remains.

Bayshore Yard 

To replace the small and outdated yard in downtown San Francisco, SP elected to build an extensive yard at the site of a lagoon next to San Francisco Bay. In building the yard, construction crews filled in the lagoon with spoil from the rural work of the Bayshore Cut Off. This yard became the major classification yard for the San Francisco Terminal. Upon arriving at Bayshore freights had their cars switched out into cuts for the various industrial areas. 

From Bayshore, switch engines hauled the cuts of cars to the small yard in South San Francisco and to Mission Bay yard at 16th and Bryant streets in downtown San Francisco. After dropping off these inbound cars, engines would return to Bayshore Yard with cuts of outbound cars that would eventually be made up into outbound trains.

San Francisco-bound Train 139 skirts around Bayshore Yard with Train Master 3030 in charge on April 8, 1972 . In the background are sidelined passenger cars no longer needed with the advent of Amtrak. (Jon Porter Photo)