She has taken over from Alan Yentob, who becomes BBC Director of Television, but the post has been renamed and redrawn to include more business responsibilities, alongside creative and editorial ones.
Ms Bennett, married with a son and a daughter, becomes the most senior programme-maker at the BBC and one of only a small number of women at her level and above.
As head of science, Ms Bennett was responsible for programmes including Animal Hospital, Ice Mummies, Trust Me I'm A Doctor and Horizon. Her programme Fermat's Last Theorem won a "best documentary" awars from Bafta, as well as the Prix Italia this year. Since last September she has overseen the BBC's network radio and World Service science units. In her new job, she will develop new BBC services, including digital channels and on-line broadcasting.
Chosen by the BBC Board of Governors, Ms Bennett also becomes deputy chief executive of production and a member of the BBC Board of Management.
BBC Production chief executive Ronald Neil said: "Jana shone through amongst an impressive list of candidates. She will ensure that BBC Production is a place where the strongest ideas and the best programme-making talent are encouraged, developed and valued."
Ms Bennett said: "The programme-making talent within the BBC is the future of the BBC. I care passionately about the programmes we make and the people who make them."
American-born Ms Bennett was educated at Bognor Comprehensive in West Sussex, Oxford University and the London School of Economics. She joined the BBC as a news trainee in 1979 and worked in local, regional and national newsrooms, on Nationwide, The Money Programme, Newsnight and Panorama, going on to science and the editorship of Horizon.
Mr Yentob said: "I am a great admirer of Jana Bennett. This is a terrific appointment for BBC Production and for our radio and television networks."
Mr Yentob took the job of director of television, overseeing BBC1, BBC2 and forthcoming digital services, when Michael Jackson left earlier this year to become head of Channel 4. Mr Jackson's departure also left a vacancy for Controller of BBC1, which is expected to be filled later this month.
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