The diameter line (Durchmesserlinie) runs through the new Löwenstrasse station, as part of a two-billion-franc ($2.26 billion) plan that is the biggest urban construction project in Switzerland.
S-bahn trains on three routes began carrying commuters through the station and the Weinberg tunnel upon the completion of the first phase of a cross-city link.
Rail traffic functioned “without a hitch” on Monday morning during the commuter period, SBB said.
The 9.6-kilometre route and station, financed by the federal and Zurich cantonal governments, took seven years to complete.
SBB said crews excavated 350,000 tonnes of earth and poured 150,000 cubic metres of concrete to build the Löwenstrasse station, which features 45 new shops.
The station, 16 metres below platforms 4 to 9 of Zurich's main train station (Hauptbahnhof), is designed to handle 460 trains a day, including 320 commuter trains and 140 long-distance ones.
The new line expands local train service through Switzerland’s largest metropolitan region, which in turn is expected to improve the flow of cross-country rail traffic.
Related work will see the nearby Oerlikon train station expanded in a project set to be completed by the autumn of 2016.
“The commissioning of the diameter line is groundbreaking for our customers, who can benefit from shorter travel times, more comfort and additional connections,” Andreas Meyer, CEO of state-owned SBB said in a statement.
“We are proud of this two-billion-franc project, which can be described as a masterpiece.”
SBB said 200,000 visitors attended an opening celebration for the diameter line on Saturday.