Trains began running between Pleasant Hill and Pittsburg Bay Point in Contra Costa County just after 8 a.m. Sunday, Agency spokesman Jim Allison said in a statement.
Service had been suspended Friday evening after an out-of-service train derailed on an elevated stretch of track as it was leaving the Concord Station and going to Concord Yard.
The 10-car train was under computer control but when it headed into a switching mechanism, the first four cars were thrown off the tracks.
Only the train operator was aboard and was not hurt in the accident.
Buses provided by AC Transit, Tri Delta and Contra Costa County Connection served the closed BART stations on Friday and Saturday, and one shuttle train was operating.
BART removed all four of the derailed cars and trucked them to maintenance facilities for repairs on Saturday, and crews finished repairing and testing the marred tracks early Sunday morning, Allison said.