The team announced the details Thursday, including a mutual, $15 million option for a sixth year.
General manager John Mozeliak said the Cardinals consider Molina to be the best catcher in baseball and team Chairman Bill DeWitt Jr. called him "a signature player, franchise-type player." The contract makes Molina the second-highest paid catcher in the majors, trailing only the Twins' Joe Mauer (eight years, $184 million).
"I grew up here, I feel good here," Molina said. "It was my first choice to stay here."
He won his second World Series with St. Louis last fall and said, "I'm happy to be a Cardinal for 5-6 more years. I'm looking to like six more championships. This is a great organization."
Talks accelerated after Molina's longtime agent, Melvin Roman, arrived at the team's spring training site last week. Roman has represented the catcher since he signed his first contract with St. Louis in 2000, when Molina was a fourth-round pick. Both parties said it was easier dealing face to face.
"The whole process was very easy," Roman said. "We worked very hard to get it done."
The 29-year-old Molina is a lifetime Cardinal and one of the best defensively at any position, winning a platinum glove last season in voting by fans. He also is coming off the best offensive season of his career.
Molina batted .305 in 2011 with 14 home runs and 65 RBI, and added 12 RBI during the team's World Series title run. He has been durable, too, averaging 138 games the past three seasons.
Put it all together, and the body of work stood out for the Cardinals.
"He's at the peak of his career and we're just thrilled to have him," DeWitt said. "He's a premium player, plus he plays so much. We were both highly motivated to get this done."
New manager Mike Matheny was a three-time Gold Glove catcher for St. Louis from 2000-04, leaving for free agency in 2005 after losing his job to Molina. He said Molina came to camp motivated and has set the tone for younger players.
"I don't think you can have any expectations higher than he has for himself," Matheny said earlier in camp. "I can honestly say I've watched him quite a few years and I don't think I've seen him work as hard. ... I think certain players have the ability to push themselves beyond contracts, beyond recognition."
The Cardinals had been saying since the start of spring training that they were hopeful of reaching a deal. Molina came to camp with a stance hardened by close friend Albert Pujols' departure for a free-agent deal with the Angels, and said the team would not get a hometown discount.
Earlier in camp, Molina said Pujols was like a big brother to him, and that the failed negotiations in St. Louis definitely affected him. But he also has emphasized he's happy in St. Louis, and that his absence from the team's Winter Warmup fan festival and the team's White House appearance were simply because he had other commitments.
The Cardinals had offered Pujols more than $200 million over 10 seasons, and have used those funds and more to build a contender without the three-time NL MVP. Outfielder Carlos Beltran signed a two-year, $26 million free agent deal and shortstop Rafael Furcal re-signed, getting a two-year, $12 million contract.
St. Louis has payroll flexibility going forward, with contracts totaling more than $30 million for first baseman Lance Berkman and pitchers Kyle Lohse and Jake Westbrook due to expire. The team has a payroll of around $115 million heading into this season.
Molina is the youngest and most talented of three brothers to catch in the major leagues. His arm has been particularly deadly on pickoff picks at first base with Pujols, but he'll need to develop teamwork with Berkman this season.