Toronto FC extended their lead atop the league standings with the victory. Toronto is 7-0-2 over its last nine games.
The heartbreaking defeat cost Atlanta an opportunity to move over the playoff line. Atlanta United remains a point back of the Chicago Fire for the 10th and final Eastern Conference playoff spot.
Atlanta United is winless in their last four (0-2-2) games, scoring just one goal in that stretch.
Toronto goalkeeper Quentin Westberg needed to make only one save for his sixth shutout of the season, but it was a critical stop. In the 68th minute, Brooks Lennon sent a quality cross into the box for Erick Torres, and the striker's header would have landed inside the post had Westberg not been in position for the block.
Both teams were playing for the fifth time in 16 days, and a bit of fatigue was apparent in a game short on premium scoring chances. Toronto and Atlanta each used the maximum five substitutes to try to add fresh legs to their lineups.
Atlanta designated player Ezequiel Barco entered the game as a half-time substitution, returning after missing seven games with injury.
Michael Bradley made his return to Toronto FC's lineup, coming off the substitute bench to replace Jonathan Osorio 20 minutes into the game. Bradley missed Toronto's previous nine games due to a right MCL strain.
Toronto coach Greg Vanney said during a halftime interview that Osorio was "a precautionary sub," as Osorio was feeling some leg tightness. Entering Sunday's action, Osorio was third among all Toronto FC players in minutes (1,343) this season.