Three games into his Cardinals' career, he suffered a broken left thumb in a game against his former team, the Pirates. He missed more than a month and returned to post a career-low batting average of .214. Nevertheless, the Cardinals won the National League Eastern Division crown with Peña rebounding to post a .381 batting average in the 1987 National League Championship Series as, the Cardinals defeated the San Francisco Giants. In the 1987 World Series against the Minnesota Twins he produced 9 hits with 4 runs batted in as the Cardinals lost in a seven-game series.