The 44-year-old Mozeliak will now be with the Cardinals through 2016. Matheny, in the second year of a two-year contract, is now guaranteed through next year. Terms were not announced.
"We just wanted to solidify their standing in the organization and keep the continuity of the baseball operations going," chairman William DeWitt said, adding that the vision of the organization is to "win a championship but not at the expense of mortgaging our future."
Mozeliak was named senior vice president and GM in October 2007. Since then, the Cardinals have reached the postseason three times, winning the 2011 World Series and coming within a game last season.
Mozeliak, an 18-year veteran of the Cardinals front office, is credited with acquiring players such as All-Stars Matt Holliday, David Freese, Carlos Beltran, Lance Berkman and Rafael Furcal in his five years as GM. He signed All-Star catcher Yadier Molina to a long-term deal last spring.
"Since taking over in 2007 the results on the field speak for themself," DeWitt said of his GM. "Beyond that we have total alignment on our vision for this organization and that is to compete year in and year out at the major league level and we know the only way to do that consistently is to have a strong player procurement and development program.
Matheny, who guided the Cardinals to a wild card berth and the NLCS in his first year as a manager, said picking up the option "wasn't something on my radar."
"I had to shake my head a couple of times because I really didn't know that was a topic of conversation," said Matheny, 42. "I felt like I had a lot to do and a long way to do and I still feel that way. It's special to be wanted to be a part of this organization moving ahead."
Mozeliak praised Matheny for how he stepped in for Tony La Russa, who retired after the 2011 season after 16 years with the Cardinals.
"Even though his learning curve had to be very quick given his experience level coming into this he did an amazing job," Mozeliak said. "I really believe his future is really bright and I really believe this group is positioned to have a lot of success in the future."
The Cardinals were 88-74 in Matheny's rookie year. After defeating Atlanta in the wild-card playoff, they eliminated the Nationals in five games in the division series and lost Game 7 of the NLCS to the Giants after taking a 3-1 series lead.
"They've given us an opportunity and given us the personnel to go out and compete every year and this year is no different," Matheny said. "And you look at the talent that has been developed and is on the way it's exciting to think about the future."