A second doctor's opinion confirmed the 29-year-old, right-handed starter will require the replacement of the ulnar collateral ligament in his right elbow, Cardinals general manager John Mozeliak told reporters at the team's spring training site in Jupiter, Florida.
Typical recovery time for the procedure, known as "Tommy John surgery," is roughly 12-15 months for pitchers.
"It's not a real surprise to us but certainly a disappointment and a finality to this process," Mozeliak said.
The 6-foot-7(201cm) Wainwright is expected to have the operation next week.
The procedure is named after a former Major League pitcher who became the first professional athlete to successfully undergo the surgery.
Wainwright said he felt a sensation in his elbow while throwing batting practice on Monday and the problem developed into significant stiffness.
The pitcher went 20-11 in 2010 and finished second to Philadelphia's Roy Halladay in voting for the NL Cy Young Award. He was third in 2009 voting, when he had a 19-8 record.
(Reporting by Gene Cherry in Salvo North Carolina; editing by Simon Evans in Miami)