Lynn (6-1) walked five in the early going but later settled down, holding the Mets to three runs over seven innings. The right-hander yielded four hits while striking out seven in a career-high 124-pitch performance.
With the score tied 3-3 in the seventh, Ty Wigginton pinch-hit for Lynn and stroked a one-out double off reliever Scott Rice (1-3). He came home when Matt Carpenter's comebacker deflected off Rice for a run-scoring hit.
Matt Holliday followed with a two-run homer to ice the triumph for the Cardinals, who took the opener of a four-game series.
Carpenter finished with two RBI in the victory.
Daniel Murphy went 3-for-4 with a two-double for the Mets, who dropped a fourth straight.