The southbound train apparently struck a large piece of metal on the tracks between South San Francisco and San Bruno at about 7:30 p.m., Caltrain spokeswoman Christine Dunn said.
A tank on the engine was damaged, causing a leak of diesel fuel, Dunn said.
No one was injured.
North and southbound trains were delayed until crews cleared the northbound side for single-track service at about 10:15 p.m.
Hazardous materials crews continued to work overnight, and Caltrain was cleared for regular service this morning, Dunn said.
At about 9:30 a.m., a southbound train broke down near the San Antonio Station at Mountain View and was taken out of service, Dunn said.
The problem was unrelated to Saturday's spill, which remains under investigation, she said.