Dutch team was beaten in all three of their matches in the tournament and finished bottom of Group B.
Bert van Marwijk, 60, refused to answer questions about his future last week but his departure has now been confirmed by the Dutch FA.
Bert van Marwijk led the Netherlands to the 2010 World Cup final in which they were beaten by Spain in extra time.
“I have severe doubts, but have decided to take this step anyway,” Bert van Marwijk said in a statement.
The head of the KNVB (the Dutch FA), Bert van Oostveen said: “The KNVB are grateful to Van Marwijk. I personally had a very good feeling about our co-operation.
“Of course it is sad to part early, but we must be realistic.”
The Netherlands won nine of their 10 qualifying matches for Euro 2012, rising to the top of the FIFA world rankings in August 2011.
But drawn in the “Group of Death” with Denmark and eventual semi-finalists Germany and Portugal, they lost three consecutive competitive games for the first time in their history.
A 1-0 opening defeat by Denmark was followed by 2-1 defeats against Germany and Portugal.
The performances were in stark contrast to their displays at the 2010 World Cup, in which the Dutch took maximum points in Bert van Marwijk’s first tournament as coach.
The Dutch went on to reach the final, but Bert van Marwijk’s negative tactics in a bad-tempered game against Spain led to criticism from the media and Dutch legend Johann Cruyff.
Bert van Marwijk, who has previously coached Feyenoord and Borussia Dortmund, had taken over from Marco van Basten in 2008 and had a contract that ran until 2016.
The Netherlands have a friendly against Belgium on 15 August before starting their 2014 World Cup qualifying campaign against Turkey in September.
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