The 31-cap Germany defender left Stuttgart as a youngster to join Bayern in 2002 and won five top-flight titles and the UEFA Champions League with the German giants.
He has been blighted by injuries in recent seasons and spent part of last term on loan at Schalke, before his contract at the Allianz Arena expired in June.
The 28-year-old was delighted to come back to a club that holds a special place in his heart.
"Nobody should forget their roots and I never did," he told the club's official website.
"The VfB was and is something special for me and has filled me with emotion again immediately."
Stuttgart won the 2. Bundesliga last season with Hannes Wolf at the helm.