The race was headlined by a huge multi-car pile-up at turn one which brought out the red flag.
All drivers were unhurt in the incident, though Santino Ferrucci suffered a scary moment when he went airborne having been unable to avoid Pato O'Ward.
Herta shares IndyCar annoyance after win
Herta has finished in the top five six times this year, including runner-up on two occasions.
The victory boosts the 24-year-old to fourth in the drivers' standings, 57 points behind leader Alex Palou, who came home fourth in Toronto.
The win comes as a relief for Herta, but the Andretti driver would have liked to be able to capitalize on his momentum sooner.
“We have been knocking on the door of a win for so long, 41 starts without a win is a long time," Herta told Honda Racing.
"It has been disappointing for us, we are a team with an owner who demands perfection and results.
“Man, I am so happy, this Gainbridge Honda was so fast, and finally we got a win after such a long time it feels so good.
"I wish we did not have this long break now I want to go right back in and win another one.”
The race was affected by a number of cautions as well as the red flag, but Herta was delighted with how he and the car dealt with all conditions.
“I struggled a little bit, this place and any of that have concrete the tires just feel like you are on ice when you hit that," he said.
"For us the car was great on everything, it was great on red tires and black tires, great on restarts, long runs, and saving fuel, whatever I needed to do it let me do.”