The 41-year-old, who has been in caretaker charge at The Valley since March, has signed a contract until the end of the season.
He guided the Addicks to the semi-finals of the League One play-offs in May after replacing Karl Robinson.
"I'm delighted and very proud to be appointed manager," Bowyer told the club's website.
"I said when I first took charge that it was a fairytale to be back working at Charlton, the club I started playing at.
"I love the club and will give everything to get promotion."
Charlton are currently 10th in the third tier having taken eight points from their opening six games ahead of Saturday's meeting with Wycombe.
Club director Richard Murray said: "This appointment is something he deserves because of his hard work and success in the role already.
"He has created a real togetherness amongst the players and fans and I'm really pleased the owner has taken the decision to appoint him as permanent manager."