The three players thus became free agents and could sign with any club, including the Cardinals.
Flores had an inconsistent season, finishing with a 5.26 ERA, a 1-0 record and one save in 43 games. Johnson is coming off shoulder surgery.
Miles, a switch-hitter, batted .317 (120-for-379) in 134 games. He was also non-tendered last year but re-signed with the Cardinals for $1.4 million.
All three were eligible for salary arbitration. Five other players in that category, outfielders Rick Ankiel, Chris Duncan and Ryan Ludwick and pitchers Brad Thompson and Todd Wellemeyer, were tendered contracts.
The moves leave the Cardinals with 34 players, six below the maximum 40.
The Cardinals didn't immediately release a statement about the moves.
Dick Kaegel is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.