Heyward finished off a big night in which he doubled home a run in the sixth and then scored on a balk by reliever Luis Perez.
Toronto forged a 3-3 tie in the eighth when Edwin Encarnacion scored on a groundout by Yunel Escobar, but Heyward was again in the middle of the action when Atlanta came up with a walkoff victory -- its fifth consecutive win.
Heyward beat out an infield single to open the 10th against Francisco Cordero (1-4) and advanced to second on a sacrifice by pinch-hitter Jack Wilson. With Andrelton Simmons at the plate, Heyward broke for third and then took advantage of Arencibia's wild throw to score the winning run.
That made a winner out of Cristhian Martinez (3-1), who walked one and struck out two in the top of the 10th.