The Bavarian Administrative Court turned down 17 cases filed against the building of the new runway, which will increase airport capacity by 30 flights a day, in front of a courtroom filled with 300 angry protesters.
Shouting broke out when it was announced that despite a 2012 referendum voting against the runway, legally there was nothing to stop construction beginning.
Judge Erwin Allesch said that a third runway – plans for which have been in the pipeline for years – would not be detrimental enough to the environment nor disruptive enough for those living nearby, for it not to be built.
As soon as plans were announced in 2011, protesters joined forces in an attempt to stop them. It was, they said, a pointless venture as the number of flights taking off and landing at the airport had been dropping every year.
The new runway will be four kilometres long and stretch out to near the suburb of Freising.
Dr Michael Kerkloh, chairman and CEO of Munich Airport's operating company, said: "This is an extremely important signal for the future development of Munich Airport.
"The ruling underscores the fact that our planning, including the extensive measures taken to protect people and nature, have stood up to an exacting review by an independent court."
He added in a statement: "Munich Airport still has the opportunity to handle the projected traffic growth in the coming years and maintain its position among Europe's major air transportation hubs."
Airport union ADV welcomed the court's decision to give construction the go-ahead. “It is a good sign for airports everywhere in the country,” said union head Ralph Beisel.