The 41-year-old, who took over as caretaker manager from Karl Robinson in March, signed a contract until the end of the season.
Bowyer helped Charlton win 6 of their final 10 games last season, taking them from 9th to 6th, before losing to Shrewsbury in the play-off semi-finals.
"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," Bowyer said.
At the end of last season, Bowyer said that he would only continue to manage the club if he was given the job on a permanent basis. However, after starting this season as caretaker manager, he has guided Charlton to 10th place, winning 2 out of 6 league games.
"We got the players in that we wanted this summer and this now gives us the stability. The players and the staff have been brilliant and I am looking forward to continuing working with them as together we aim for promotion," Bowyer continued.
"The fans have been outstanding too and I want to thank them for all their support at the end of last season and the beginning of this season. They have supported me from that first minute of my first game against Plymouth and we all want to do well for them."