On December 16, 1988, Thompson was traded to the St. Louis Cardinals, for Steve Lake and Curt Ford,[4] where he spent four years and posted his highest batting average ever, .307, in 1991.

As a key component in the Phillies’ unexpected, last-to-first 1993 National League Championship team, Thompson platooned in left field with Pete Incaviglia, in the World Series, against the Toronto Blue Jays.

Then, crowning his day — and quite possibly his big league career: With the game on the line and the Phillies ahead 5-3, in the bottom of the eighth inning and two out, the Padres had the bases loaded, bringing their slugging right-handed catcher, Bob Geren, to the plate.

David West, the Phillies’ left-handed relief pitcher, delivered a choice fastball that took a long ride, sailing over 370 feet (110 m) from home plate, and above the wall in left-center field.

The fleet-footed Thompson arrived just in time, planted his feet, and made a surreal leap – seemingly sensing in some sort of inexact prayer, where the ball was – and cradled it into his glove's web, retiring the side and preserving another Phillies win, in that magical 1993 season, high-fiving center fielder Lenny Dykstra all the way to the visiting dugout.

[6] During Thompson's tenure as batting coach, the Phillies have led the league twice in runs scored, even though they have alternated between only 2nd and 3rd place in their respective division due to pitching difficulties.

Having played for the 1993 National League Champions, Thompson joined Larry Bowa and John Vukovich as the only Phillies in franchise history to go to the World Series as both a player and coach for the club.