Riding a six-game unbeaten streak, the Fire extended that run thanks to Luis Solignac and Nemanja Nikolic at Toyota Park.
After Hector Villalba came close to opening the scoring for Atlanta, Solignac broke the deadlock just shy of the half-hour mark.
David Accam showed great composure as he rounded the goalkeeper and teed up Solignac, who side-footed home.
The league's leading scorer – Nikolic – then took his tally to 12 for the season courtesy of a 70th-minute penalty after Tyrone Mears handled the ball in the area.
With a sixth successive home victory, second-placed Chicago moved within a point of Eastern Conference leader Toronto FC.
Portland is two points adrift in the west thanks to Fanendo Adi's brace at home to Dallas.
42 days between goals 6 & 7.— Major League Soccer (@MLS) June 11, 2017
40 minutes between goals 7 & 8. pic.twitter.com/fPKidkeJ32
Adi scored in either half at Providence Park as the Timbers recorded back-to-back wins in MLS.