The decision was confirmed Sunday by spokesmen for both the New York Yankees and Major League Baseball.
Red Sox manager Alex Cora briefly pulled his team off the field in the sixth inning Saturday night after Verdugo was struck in the back by a ball thrown from the left-field seats. He was not hurt.
"While the Yankees appreciate the spirit and passion of our fans in our various rivalries -- especially with the Red Sox -- reckless, disorderly and dangerous behavior that puts the safety of players, field staff or fellow fans in jeopardy will not be tolerated," the Yankees said in a statement on Sunday.
"There is absolutely no place for it at Yankee Stadium. The safety of everyone at Yankee Stadium, including guests in the stands and players on the field, will always be the top priority for the Yankees organization every time we open our doors."
An angry Verdugo shouted at the crowd and was restrained by Boston first-base coach Tom Goodwin as Saturday's contest was held up in a driving rain. The fan, who was not identified, was ejected from the ballpark.
"When I went out there, it was loud, and it got nasty -- from both sides,'' Cora said Sunday. "I just needed to calm him down. That was the whole reason that I just took everybody off the field. I'm like, where he's at right now mentally, he's not going to be able to play right now. No chance.''
Verdugo said he tossed the ball into the stands to a young Red Sox fan but that a Yankees fan intercepted it and threw it back onto the field, hitting the outfielder.
"It's awful, embarrassing, unacceptable," New York manager Aaron Boone said afterward.
Verdugo returned to left field when play resumed following a discussion with umpires near Boston's dugout.
"It felt like it was targeted towards me, and it don't sit well with me," he said.
New York won 3-1 in a game called after six innings due to heavy rain.
"Obviously, the player was upset, understandably so,'' umpire crew chief Jeff Nelson told a pool reporter Saturday night. "We tried to make sure that there was a security presence in left field, that the issue was addressed by security, and then also balancing that with continuing the game and keeping the game moving, knowing that we had continuous rain.''
NJ.com reported Sunday the fan was not arrested.
"I'm surprised that nothing has happened, let's put it that way,'' Cora said.
"I'm just glad that [Verdugo's] OK. He saw the video and all that, I guess, and he's OK,'' the manager added. "Obviously, yesterday, it wasn't great for the game, it wasn't great for the people here. I know how bad they feel. Hopefully, it's the last time that something like that happens.''