The 29-year-old, who has torn cruciate ligaments twice in his career and has spent much of the last two and a half years sidelined by injury, makes the move to Cologne for an undisclosed fee.
"We're pleased to have found a solution which suits everybody," Bremen director of sport Klaus Allofs said.
"Cologne is Patrick's home, which is why he has opted for this transfer. We wish him all the best for his future."
The former Germany striker scored 35 goals in 65 games in a Cologne shirt between 2005 and 2008, prior to a move to Bayer Leverkusen and his first serious knee injury.
He scored 13 goals in 28 appearances for Wolfsburg, the last of which came in April.