Atlanta (11-9-9, 42 points), which vaulted up the table into a playoff spot with the win, has won two of its past three games.
Toronto (6-16-7, 25 points) had its four-game unbeaten run end and was officially eliminated from playoff contention with the loss.
Toronto held the early edge in possession and in the fourth minute, nearly opened the scoring when midfielder Jonathan Osorio's shot from the top of the box hit the crossbar.
Atlanta struggled to hit the target early in the first half, going more than 17 minutes before getting a shot on goal. But the visitors found their legs as the half progressed.
Luiz Araujo struck in the second minute of first-half stoppage time to give Atlanta a 1-0 lead. Araujo took a feed from defender George Bello inside the box and sent it over Bono's right hand into the back of the net.
United continued to press in the second half.
Araujo nearly had his second of the match in the 51st minute but his shot was stopped by defender Omar Gonzalez, who stood at the goal area after Bono was out of position. Marcelino Moreno had a chance in the 55th minute but Bono jumped to get his hands on the ball for the save.
Gonzalez nearly leveled it for Toronto with a header in the fourth minute of second-half stoppage time but was denied by goalkeeper Brad Guzan.
Moreno made it 2-0 in the seventh minute of second-half stoppage time with a kick that went far side.