Hawkins, who was also fined an undisclosed amount, will appeal, MLB said. The New York Daily News first reported that Hawkins would be suspended.
The penalty had been set to begin Thursday, when the Yankees hosted the Orioles.
Hawkins threw high and inside to Scott in the sixth inning of the Orioles' 12-2 blowout win on Tuesday, three innings after Yankees captain Derek Jeter was hit by a pitch. Scott, who got out of the way, felt the throw was intentional, while Hawkins said he was merely pitching Scott inside.
"If anybody knows me, and a lot of guys around this league know me, I'm not that type of person," Hawkins said on Tuesday. "He thought what he wanted to think. The way it looked, he had a reason to think like that. But it wasn't intentional."
But Scott believed that Hawkins was retaliating.
"Of course it was [intentional]," Scott said after the game. "I understand there's certain things that happen in this game. You want to protect your players, and there's a certain way to go about it. That was not it. You never throw at someone's head with intention. You can end someone's life. You can end a career."
It was the second time this season a Yankees pitcher has been suspended for a high throw that did not hit a batter. Kyle Farnsworth was suspended for throwing behind the head of Boston Red Sox outfielder Manny Ramirez. He had his three-game suspension reduced to one game by baseball executive vice president John McHale Jr., who reviewed the decision by vice president Bob Watson.
Hawkins hoped to get a similar result.
"I should, I don't know why not," Hawkins said.
Hawkins is 1-0 with a 5.57 ERA in 17 games in his first season with the Yankees. He has not hit a batter in 21 innings.
"I was a little bit surprised" that Hawkins drew a three-game penalty, Yankees manager Joe Girardi said. "Guys have been throwing inside for a long time. I think you're trying to set a precedent where no one gets hurt badly."
Information from The Associated Press was used in this report.