St. Louis opened the scoring just four minutes into the match when Rafael Navarro headed home from close range to give CITY SC an early 1-0 advantage.
The Red Bulls looked to respond but were unable to find the back of the net. New York finished the night with 11 shots, including five on target, but St. Louis goalkeeper Roman Bürki made four saves to preserve the shutout.
The match remained within reach for most of the second half before St. Louis found another breakthrough late. Simon Becher doubled the lead in the 87th minute after capitalizing on a Red Bulls turnover.
Just minutes later, Tomáš Ostrák added a third goal in stoppage time to complete the 3-0 victory for St. Louis.
The result extended St. Louis CITY SC's unbeaten run and marked the club's first victory over Red Bull New York.
For New York, the loss ended a stretch in which the Red Bulls had won their previous two matches. The team will now look ahead to its next home match against San Diego FC on October 10.