Drivers of both passenger and freight trains stayed home Friday and were not to return to work until 2 a.m. (0100GMT) Saturday. Passenger drivers started their strike early Thursday, while freight drivers walked off their jobs midday Wednesday.
The action by the GDL union has affected millions of commuters, with only a third of regularly scheduled trains running in greater Berlin, Frankfurt and Stuttgart, Deutsche Bahn said. Roughly 20 percent of all commuter trains in the former East Germany were running, while half of trains in the former West were circulating as normal, according to the train operator.
Hardest hit were freight customers, with a backlog of 43 hours affecting depots from Hamburg to Munich, according to Deutsche Bahn.
"There are still grave reductions," said Ina von Spies, a spokeswoman for the Hamburg harbor.
In a dispute that has simmered for months, GDL wants a hefty pay increase for train drivers and is insisting that they be given a pay deal separate from that given to other railway employees - a demand that Deutsche Bahn firmly rejects.
GDL has rejected a 4.5-percent raise that Deutsche Bahn agreed with two rival unions that represent a broader range of railway workers.
Deutsche Bahn has said its existing offer amounts to a raise of up to 10 percent for train drivers, along with better working conditions.
The German government and industry groups both have urged the two sides to return to negotiations, expressing concern about the possible economic fallout.