The 47-year-old former Blackburn Rovers and Blackpool boss, who has been out of management since resigning as Pool manager at the start of the season, has become the Bantams' fourth manager/head coach in 13 months following the dismissal of Stuart McCall in February 2018.
The likes of Steve Evans, Paul Hurst and Kevin Nolan had also been linked with the position.
Bowyer has been handed a brief to save Bradford's season, with the club six points adrift of safety towards the bottom of League One with 11 matches to go.
The Bantams, under the interim charge of first-team coach Martin Drury, crashed 5-1 at Portsmouth on Saturday, extending their winless sequence to five matches.
The previous weekend saw David Hopkin tender his resignation in the wake of a bitter 3-2 defeat to ten-man Walsall.
Bowyer's first game in charge will be at home to play-off chasing Peterborough United on Saturday.
City have won just once in their past nine league outings.
Bowyer will be assisted by Andy Todd, son of former City chief Colin.
He said: “I’m absolutely delighted to be here.
“It’s a massive club and the opportunity to manage Bradford City doesn’t come along that often – it was one that I had to take.
“I’ve been ready to get back into management for a while but it’s been about getting the right opportunity. This is a fantastic one for myself and for Andy.