In 1989, Thompson's batting average dropped to .241. However, he led the National League with 11 triples and scored a career-high 91 runs while hitting ahead of Will Clark and Kevin Mitchell in the batting order. The Giants once again won the Western Division crown and faced the Chicago Cubs in the 1989 National League Championship Series. Thompson hit 2 home runs in the series including a game-winning two-run home run in Game 3 as the Giants went on to win the series in five games. Thompson was held to only one hit in the 1989 World Series against the Oakland Athletics as the Giants were swept in four straight games.