The engine of train No. 324 died at the San Bruno station, according to spokeswoman Mary Knuckles. That train subsequently coupled with train No. 226 to be pushed out of the way.
Northbound delays continue as well, after a broken rail just south of Morgan Hill disrupted service around 6:30 a.m.
Caltrain set up a bus bridge for riders between the Gilroy and Diridon stations.
That problem has since been resolved and northbound trains are being allowed through, but there are still delays, Knuckles said at about 9:10 a.m.