"The terrorist attack on Theo van Gogh has unleashed feelings of great fear and insecurity in [Dutch] society", presiding Judge Udo Willem Bentinck said.
Van Gogh, well known for his scathing criticism of Islam and the multicultural society, was shot and stabbed in broad daylight as he cycled the streets of Amsterdam on 2 November 2004.
His murder stoked ethnic tensions in the Netherlands and sparked a wave of reprisal attacks mainly directed at the Muslim community.
"There is only one fitting punishment in this case and that is a life sentence. You are thus sentenced to life in prison," the judge told Bouyeri.
A life sentence carries no possibility of parole in the Netherlands.
Bouyeri nodded after the verdict was read out.
He shook hands with his lawyer and left the courtroom without looking in the direction of van Gogh's family members who were also present in the Amsterdam high-security court.
Van Gogh was well-known for his
scathing criticism of Islam
During the trial two weeks ago, Bouyeri told the court that he killed van Gogh out of his beliefs.
He insisted that "the law compels me to chop off the head of anyone who insults Allah and the prophet" and asked for the maximum sentence.
"I can assure you that if I am ever freed, I will do exactly the same," he vowed.
The court painted Bouyeri as someone with "radical beliefs, and obsession with violence and totalitarian views".
The 27-year-old was convicted of murdering the filmmaker and obstructing the work of liberal lawmaker Ayaan Hirsi Ali and threatening her with a terrorist act, both crimes committed with a terrorist aim, according to the court.
He was also convicted of the attempted murder of several police officers and bystanders and illegal possession of firearms.
Van Gogh, a distant relative of 19th century painter Vincent van Gogh, together with Hirsi Ali had made a short film called Submission, linking Islam to the abuse of women, which caused outrage in the Dutch Muslim community.
Bouyeri threatened Ayaan Hirsi
Ali, who worked with van Gogh
After van Gogh's murder, Hirsi Ali went into hiding for three months because a letter threatening her and other politicians was found on the filmmaker's body.
"The defendant has deliberately tried to instil fear in the Dutch population," the court said in its ruling.
"The killing was carried out in a gruesome way in a busy street, during rush hour, the victim was a celebrity. Add to that the letter left on the scene containing threats not only to Hirsi Ali but to the Netherlands as a whole."
The prosecution had demanded that Bouyeri be stripped of his right to vote or to stand for election, but the court denied the request arguing that since the defendant clearly rejected democracy it was unlikely that he would ever exercise these rights.
Even though prosecutors have said that Bouyeri was "a leading figure" in a "terrorist organisation" known as the Hofstad group, he has not yet been charged for that because of a lack of evidence.
The Dutch national prosecutor's office is expected to decide soon if Bouyeri will be separately prosecuted for membership of a terrorist organisation.
They have already charged 15 other people with being members of the Hofstad group.