The singer topped a public vote at the end of the 10-day Channel 4 charity special.
He was rated favourite by bookmakers to win the series, which saw six personalities live inside a camera-filled house.
Les Dennis was the second-placed finalist, while Messenger came third.
Speaking to presenter Davina McCall in front of a cheering crowd, quietly-spoken Owen, who has been largely out of the public eye since Take That split in 1996, joked: "I'm a bit out of practice, sorry."
He said he had hoped Dennis would win the contest.
"He'd been through a lot, he was a star and he helped me get through it."
He said of his experiences in the house: "I had a moment where I woke up, and at one end of the room Les Dennis was shaving, and at the other end Goldie was putting on his aftershave.
"I thought - what am I doing here?"
Emotional
Dennis, whose emotional outbursts in the house stunned viewers, cried as he saw a video of his wife Amanda Holden - who was away filming - congratulating him on his success.
He embraced his son Philip - the subject of much of his conversation after he admitted he did not see him enough.
"Just coming out and seeing the reception was amazing, fantastic. I had the best time, it was brilliant," Dennis told presenter Davina McCall.
"I wanted to go in and be me - and I probably was, obviously. I've hosted a game show for 15 years and everyone sees a cheery, smiley Les and that's not the real me."
'Aura'
As cameras showed winner Owen crying in the house alone, he said: "He's got a fantastic aura, a really brilliant aura - look at him. That's so sweet."
Messenger said after leaving the house: "I thought it'd be nice to make it to the half way mark.
"I never thought I'd ever win. I knew what I was letting myself in for."
Comedian Sue Perkins, 33, was evicted on Thursday after the public overwhelmingly voted for ex-Take That star Owen to stay.
Former daytime TV host Anne Diamond and musician Goldie were evicted by viewers earlier this week.
None of the contestants were paid for taking part, and the show will raise money for the Centrepoint homeless charity, the National Missing Persons Helpline, the Rethink mental illness charity and the Samaritans.