Stephenson (1-0) sat out all of the 2001 season after suffering an elbow injury in the 2000 playoffs and missed three months last year with a pulled left hamstring and sore left shoulder, finishing 2002 just 2-5 with a 5.40 ERA.
But he looked sharp in his 2003 debut, blanking the Brewers until giving up a solo homer in the seventh to Eddie Perez, the final batter he faced. Stephenson walked two and struck out two.
Milwaukee made it close in the ninth on Royce Clayton's three-run homer off Cal Eldred, but Steve Kline got the final two outs for his second save.
Matt Kinney (1-0) took the loss, yielding four runs and nine hits in 5 1/3 innings.
Albert Pujols homered and drove in three runs for the Cardinals, who have started 3-0 for the second time in four years.