Right-handed reliever Jorge Rondon was optioned to Triple-A.
The 26-year-old Lyons will take the rotation spot held by Joe Kelly, who was put on the 15-disabled list last week. Kelly strained his left hamstring trying to beat out a bunt.
Lyons went 2-4 with a 4.75 ERA in 12 games for St. Louis last year, including eight starts for the NL champions. He made his major league debut last season and was with the Cardinals during four separate stints.
''Hope to see him stand up there with confidence,'' Cardinals manager Mike Matheny said before the game.
Lyons was 2-0 with a 3.32 ERA in three starts at Memphis this year. He last pitched on Wednesday.
No one in the Mets' lineup had ever faced Lyons in the majors going into the game at Citi Field. Lyons will wear No. 70.
''Nobody's seen him,'' Mets manager Terry Collins said. ''Hopefully, he gets a little amped up and makes some mistakes.''
Rondon was called up from Memphis on Thursday and didn't pitch in the weekend series at Washington.