With the exception of the 1996 season, his performance while an Oakland Athletic was lackluster at best, and he was traded to the Yankees after the 1997 season for Kenny Rogers, who had struggled mightily in New York. His first year in the Bronx was his best, batting .300 with 98 RBIs and 19 home runs, particularly remarkable for a player who typically batted eighth or ninth in the order.

Although his next three years were not up to his phenomenal 1998 season, he remained a fan favorite for his spirit and clutch hitting in October. During his career with the Yankees, they won the American League pennant every year, from 1998-2001, as well as the World Series from 1998-2000. Brosius won World Series MVP Award and was an All-Star in 1998. He won a Gold Glove in 1999.

Brosius hit a dramatic, two-out, two-run home run in the bottom of the ninth inning of Game 5 of the 2001 World Series against the Arizona Diamondbacks to tie the game and set up an extra-inning Yankees win. The previous night, New York first baseman Tino Martinez had hit an incredible two-out, two-run home run to tie the game as well. It marked the first time in World Series history that this had ever occurred. The Yankees would go on to lose the series in seven games, after which Brosius retired.

Brosius was renowned throughout his career for his exceptional defensive play at third base. His trademark play was the single-motion bare-handed grab and throw to first on softly-hit ground balls and bunts.

Was given the nickname Scott "Supercalifragilisticexpiala-" Brosius by Chris Berman.