Pumas, eighth in the regular season, had knocked off top-seed Santos, 5-4, on aggregate in the semifinals but couldn't break down the stingy Atlante defense in the first leg of the finals. Former Colorado Rapids midfielder Alain Nkong came on in the 90th minute for Atlante.
The second leg will be played Sunday at Cancun's Estadio Quintana Roo (TV: TeleFutura, live, 8 pm ET).
Atlanta moved this season from Mexico City to Cancun. The Mexican league is one of the leagues in the world that allows the movement of clubs from one city to another in the tradition of American pro sports.