Martinez was diagnosed with a shoulder strain a day after leaving a start in the first inning, and the NL Central-leading Cardinals say the right-hander won't pitch again in 2015.
Rest rather than surgery was prescribed with a recovery time of between one and two months.
General manager John Mozeliak said if the injury had occurred on Aug. 1, the 24-year-old right-hander potentially could have pitched in the postseason.
"Unfortunately, where we are on the calendar, it's just not going to work out,'' Mozeliak said.
Manager Mike Matheny said Martinez was "broken up'' by the news. The pitcher had dedicated his season to late teammate Oscar Taveras, a fellow Dominican Republic countryman, who died in a car accident on Oct. 26, etching the initials "OT'' on the back of the mound before starts.
"Just a shame,'' Matheny said. "But he gets it.''
The injury is the latest hit for the Cardinals, who top the majors with a 98-57 record despite losing Adam Wainwright, Matt Holliday, Matt Adams, Jon Jay and Jordan Walden for extended periods. Third baseman Matt Carpenter left Saturday's game with hip tightness.
"Such is this game,'' Matheny said. "We're just going to have to keep rolling like so many other times this season.''
Martinez is 14-7 with a 3.01 ERA this season.
He was removed just seven pitches into his start Friday after feeling right shoulder tightness against the Milwaukee Brewers. Martinez flinched after making the first pitch to Adam Lind, the Brewers' third hitter.
After meeting with trainers and Matheny on the mound, Martinez left the field with his glove covering his face and in apparent pain.
Initial tests on Martinez's right shoulder were positive, but an MRI taken Saturday revealed the strain.
Mozeliak said the postseason rotation had not been discussed, for precisely this reason. He said Lynn's postseason experience would be a plus.
"Sometimes decisions get made for you,'' Mozeliak said.
Ace Adam Wainwright, who threw a second simulated game earlier Saturday, is not under consideration for the postseason rotation because there isn't enough time to build up his strength.
Wainwright has made a rapid recovery from a left Achilles torn in late April and is likely to get a chance to pitch in relief before the postseason.
"What we saw baseball-wise out here was very good,'' Matheny said. "It's just a matter of getting medical clearance.''
Mozeliak said Tyler Lyons, who stepped in after Martinez was hurt, is likely to inherit that spot Wednesday at Pittsburgh.
Information from The Associated Press was used in this report.