Donohue's victory at the Rolex 24 came on the 40th anniversary of his late father's win at this race, and spoiled a bid by Chip Ganassi Racing for a fourth consecutive Rolex 24 checkered flag.
Donohue passed Ganassi's Montoya with 39 minutes remaining and recorded the closest margin of victory in the race's history.
"I'm just proud that I can deliver the goods for the team," Donohue said. "I was just the guy who got to be able to do it."
The previous record for closest finish was in 2000 with a margin of 30.879 seconds.
"I was actually surprised we even fought for the win, to be honest," Montoya said. "I drove my butt off."
Joao Barbosa finished in third place, and Max Angelelli was fourth.