Munich police are still on high alert, carrying out more checks than usual at the stations, which have reopened.
A police spokeswoman said the tip-off about a planned IS suicide bombing had come from the French secret service.
The city's central station and Pasing station were closed overnight.
Police are looking for "five to seven" suspects, believed to be Iraqis and Syrians.
Munich police chief Hubertus Andrae said his force had some names which were being checked on police databases, but had no details of the suspects' whereabouts.
He urged residents of the southern German city to "carry on living as you did previously".
The alert came just hours before midnight and police in the Bavarian state capital warned people to avoid crowds.
Bavaria's Interior Minister Joachim Herrmann said the closure of the railway stations was "the right decision, because I think we cannot run any risks when we have such specific threats - a specific place and timing".
Police spokeswoman Elizabeth Matzinger told reporters that the French "gave us the hint that there was a suicide bomb attack planned for Munich during the last night at about 12 o'clock".
Police reinforcements were deployed to Munich from other parts of Bavaria.
Cities across Europe were on alert for a possible New Year's Eve attack, after IS suicide bombers killed 130 people in co-ordinated attacks in Paris on 13 November.
France and Germany are involved in the international air campaign against IS fighters in Iraq and Syria.
Security concerns had already caused New Year celebrations to be cancelled or limited in other European cities.
The authorities in Brussels called off all official events after three people were detained on Thursday in connection with an alleged New Year's Eve plot.
More than 100,000 police were deployed across France. In Paris, the traditional fireworks display was called off, but thousands of people partied on the Champs Elysees in the biggest public gathering since the November attacks.
Security was stepped up in other major European cities too, including Moscow, London and Berlin.
In Moscow, the fireworks were delayed by five minutes and, for the first time, the police closed Red Square - a traditional place for crowds to gather.
London's Metropolitan Police deployed 3,000 officers in the inner city, including extra armed officers.
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