The 30-year-old follows Richard Rufus in being forced to hang up his boots early after failing to recover from a long-term knee injury.
The former Leicester ace made just 13 appearances for The Addicks before being struck down by injury.
Addicks boss Alan Curbishley admitted it was a major blow to lose Rowett after seeing Rufus made to retire.
"I'm absolutely gutted by the news that Gary's retired," Charlton boss Alan Curbishley told the club's official website.
"He was a player of enormous ability on and off the field, and is someone we are going to miss.
"We worked enormously hard to bring him to the club and I'm so disappointed that he only managed 13 games for us.
"But it was obvious last season that he had it all to do to regain full fitness, so it is a big blow."
