Keating, controller of BBC Four, has been the favourite since Root announced her departure for the Discovery Channel in the US in March.
Jana Bennett, BBC director of television, said: "I can't think of anyone who could more brilliantly articulate why BBC Two has a special place at the heart of our national life than Roly Keating."
She added: "He has an obsessive commitment to talent on and off screen, and combines showmanship with energy and curiosity."
Bennett praised Keating as one of the pioneers of multichannel television, someone who has demonstrated a rounded understanding of what makes a channel work in growing BBC Four from scratch.
According to Keating: "BBC Two is the channel of record for British culture and being asked to take leadership of it is a huge honour, and frankly a bit daunting. But I'm also incredibly excited: it's a channel I've grown up with, and like millions of other people it's given me some of my most memorable viewing experiences."
Keating won the race for the BBC Two job against a strong field, which included: Daisy Goodwin, editorial director at independent production company Talkback; ITV controller of current affairs, arts and religion Steve Anderson; BBC controller of current affairs Peter Horrocks; and BBC Sport head of programmes and planning Pat Younge. The BBC's entertainment chief Wayne Garvie was also reported to have had an interview at a later stage.
The appointment was been overseen by BBC director of television Jana Bennett, who is also in the running for the director-general position, soon to be appointed by the corporation's new chairman Michael Grade, who takes up his position on Monday.
Keating's previous experience includes being founding producer and editor of the 'Late Show', head of programnming for BBC/Flextech joint ventue UKTV, as well as overseeing highly rated programmes such as ' The Falklands Play', 'The National Trust' and 'The Alan Clark Diaries' as controller of BBC Four.
Keating joined the BBC as a general trainee in 1983 and during his time at the corporation he has worked as producer and director in music and arts he made films for 'Omnibus', 'Bookmark' and 'Arena', including documentaries about Ealing Studios, VS Pritchett and Philip Roth.
He was a founder producer and subsequently editor of the influential arts and media magazine 'The Late Show', and from 1992 to 1997 he was editor of 'Bookmark', winning the Huw Wheldon Award for Best Arts Programme in 1993.
That year he devised and launched the long-running heritage series 'One Foot in the Past'.
His other credits include 'A History of British Art', 'The House Detectives' and 'How Buildings Learn' as executive producer.
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