Bowyer, who was assistant at The Valley under departing boss Karl Robinson, has taken temporary charge alongside coach Johnnie Jackson.
The 41-year-old made 197 appearances for the Whites scoring 55 goals in the process during a seven year stay in West Yorkshire.
“I’m very pleased to be given the opportunity to take this team forward," Bowyer told the Charlton Athletic website.
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"We have a talented squad of players and our focus has to be on winning games and giving ourselves the best opportunity to make the play-offs."
The Addicks remain just five points off the League One play-off places with a game in hand over sixth-placed Plymouth.
Charlton are subject to a takeover bid from an Australian consortium and are said to be favouring Crawley Town boss Harry Kewell, another former Elland Road player, to fill the vacant role in south London.