At a ceremony at the University of Westminster tonight (Wednesday), the British Journalism Review annual prize was awarded to the journalist by Lady Wheeler, wife of the late Charles Wheeler.
"I hope it's a recognition by my peers that I've tried to stick to my guns," said Bowen.
"I got an awful lot of support from members of the public and also colleagues," he said, of complaints partly upheld by the BBC Trust over the accuracy of his reports on Israel.
He defended his journalistic style and said he tried simply to report the story: "I haven't gone down the road of ideology, the way others have."
Mainstream media "gets a kicking in the blogosphere," Bowen said, but he's glad to be part of the profession. "I think there will still be a place for trained journalists."
Bowen said that loss of self-confidence at the BBC was not "justified." "I hope for some years in the future to continue putting noses out of joint."
"I think there's a reason that people round the world trust BBC News... We need to be proud of all that and not be defensive."
Last year's prize was awarded to BBC Newsnight presenter Jeremy Paxman.
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