The deal is reportedly worth $27 million US, an average annual value of $5.4 million.
Bouwmeester, 29, who had one year left on his current deal, joined the Blues from Calgary in a trade on April 1. In return, the Flames received minor-league defenceman Mark Cundari, goalie prospect Reto Berra and a 2013 first-round pick.
In 14 regular-season games with St. Louis, Bouwmeester had one goal and six assists. In total, he played 47 games in the lockout-shortened season, with seven goals and 15 assists.
His new deal with the Blues runs through the 2018-19 season.
The Edmonton native has a consecutive-games played streak of 635, which is the longest among active players, most for any defenceman, and fifth all-time.
He was selected third overall by the Florida Panthers in the 2002 National Hockey League Draft and has 72 goals and 235 assists in 764 career NHL games.