With the deal, one union is to hold off striking for 29 months, but the train drivers' union still has a claim. The German train service has also been criticized by the Swiss.
German rail giant Deutsche Bahn and transport union EVG struck a deal over a salary dispute overnight into Saturday, averting further strikes after travel chaos earlier in the week.
Deutsche Bahn and EVG, which represents some 160,000 rail workers, agreed on a 6.1 percent wage hike in two stages:
Deutsche Bahn also agreed to a one-off payment of €1,000 ($1,300) to the workers next year in February.
Read more: If you want German trains, go to Switzerland
The wage deal lasts for 29 months, during which EVG has agreed it cannot call a strike.
All long-distance trains and some regional trains came to a halt for four hours last Monday morning, causing chaos for travelers and commuters. The so-called warning strike threatened to expand into the Christmas and New Year's holidays.
EVG's lead negotiator, Regina Rusch-Ziemba, said the warning strike sent a clear message that resulted in "success across the board" following four days of wage talks with Deutsche Bahn.
Deutsche Bahn's head of human resources, Martin Seiler, was similarly satisfied with the outcome.
"The conclusion is an important sign of how we value our employees and a big step towards an even more modern salary and work environment," he said.
Train drivers still talking
Deutsche Bahn has still not struck a wage deal with the train drivers' union GDL, which has about 34,000 members.
However, GDL must go through arbitration before it can call a strike, meaning a walkout is off the table during the holidays, union boss Claus Weselsky said.
Swiss transport chief criticizes Deutsche Bahn
Separately on Saturday, Switzerland's transport head Peter Füglistaler criticized the German state, which is the only shareholder in Deutsche Bahn, for the low quality of the rail system and a lack of investment.
"That, I think, has partly been acknowledged," Füglistaler told Swiss Radio SRF. "But what is for us much more worrying in the short term is that the quality is so bad." Customers expect punctuality and reliability, he said.
Switzerland depends on the German rail system for a north-south European transport corridor running from the Netherlands to Italy.
Füglistaler told Swiss Radio SRF that while Deutsche Bahn maintained infrastructure, there was an investment backlog in the rail system despite increased federal funding.
Deutsche Bahn has long been plagued by late, old and overcrowded trains.
cw/jm (AFP, dpa)