Weiss, 49, just completed his first season as the Rockies' manager, guiding the team to a 74-88 record. That was last in the NL West but still a 10-game improvement over Colorado's 2012 record.
The new agreement links Weiss to the Rockies through the 2016 season. Financial terms weren't released.
"I am very excited and grateful to have the opportunity to lead this club as we work toward building a championship-level team," Weiss said in a team release.
Weiss was voted the American League Rookie of the Year in his first full major league season with Oakland. He also played for Florida, Colorado and Atlanta. He was with the Rockies as a player (1994-97).
He joined the Rockies front office and served as assistant to the general manager from 2002 to 2008. He was hired as the Colorado manager on Nov. 7, 2012.
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