David Villa opened the scoring for City, but his effort was cancelled out by a tremendous Carlos Carmona strike at Yankee Stadium. However, goals from Rodney Wallace and Maximiliano Moralez on the hour-mark secured a second straight win for Patrick Vieira's men.
Villa struck in the 17th minute with a fine finish off the post to complete a flowing team move and give City a 1-0 lead.
But a stunning volley from Carmona had the visitors level six minutes before halftime, only for City to grab control on the hour-mark.
After Atlanta had somehow held on to start the second half with numerous goal-line clearances, Wallace tapped in and Moralez followed with a finish into the bottom corner.
City sits third, just three points behind Eastern Conference leaders Toronto FC, while Atlanta are seventh.
Earlier, Minnesota United claimed a surprise 2-0 win at home to Sporting Kansas City despite seeing Bobby Shuttleworth make way early in the second half with a broken nose. Goals from Abu Danladi and Christian Ramirez secured what was just Minnesota's third win of the season and marked Sporting's second loss.
Sporting sits second in the Western Conference – level on points with leaders FC Dallas – while Minnesota jumped to seventh.