In the Western Conference, the Portland Timbers and Sporting Kansas City battled to a 0-0 draw in their opening leg.
Josef Martinez, who set an MLS record with 31 regular season goals, put Atlanta ahead in the 32nd minute before second-half goals from Franco Escobar and Hector Villalba gave them a comfortable lead to take to New York for Thursday's return leg.
The Red Bulls had a goal by Bradley Wright-Phillips disallowed early in the second half after a video review determined Alex Muyl was offside.
Hector Villalba #15 of Atlanta United celebrates scoring the third goal against the New York Red Bulls during the MLS Eastern Conference Finals between Atlanta United and the New York Red Bulls at Mercedes-Benz Stadium on November 25, 2018 in Atlanta, Geo
Image credit: Getty Images
The Red Bulls or United will host the MLS Cup on Dec. 8 as both teams had more points in the regular season than the two Western Conference semi-finalists.
The Timbers, looking to reach the Cup final for the second time in four years, were disappointed not to take advantage of their home ground on Sunday but were confident of getting a result in Kansas City.
"Definitely we wanted to get a win at home, but also they didn't get any goals,” Timbers coach Giovanni Savarese told the Oregonian.
“Now, we have to go there, make sure that we prepare with the days that we have and give everything we have to try to go through.”