The Cardinals also announced Wednesday that left-handed reliever Trever Miller had met a vesting option at $2 million for next season.
The 30-year-old Pujols led the National League with 42 home runs, won his first league RBIs title with 118 and tied Matt Holliday for the team batting lead at .312.
Pujols has led the NL in home runs and runs the past two seasons. The previous player to lead his league in homers and runs in consecutive seasons was Ted Williams in 1941 and '42.
The previous NL player to do so was Chuck Klein in 1931 and '32.
Pujols topped 400 homers last season and set a franchise record with his 39th career multihomer game.
The Cardinals were expected all along to pick up the option on Pujols' contract. The team has said there's no specific timetable for beginning negotiations on a new long-term deal with Pujols, who can be a free agent after next season.
Information from The Associated Press and ESPN Stats & Info was used in this report.