The Yankees said in a statement that Boone's procedure went "as expected," and the skipper is now in the recovery room at St. Joseph's Hospital in Tampa, Fla.
Yankees general manager Brian Cashman said Boone could return to the club in two to three days.
Earlier Wednesday, the 47-year-old Boone -- who underwent open-heart surgery in 2009 -- said in a statement that he was experiencing mild symptoms of lightheadedness, low energy and shortness of breath over the last six to eight weeks.
Boone said further tests prior to spring training indicated he had a low heart rate, leading to him having the surgery.
"My faith is strong, and my spirits are high," Boone said. "I'm in a great frame of mind because I know I'm in good hands with the doctors and medical staff here.
"... They are confident that today's surgery will allow me to resume all of my usual professional and personal activities and afford me a positive long-term health prognosis without having to change anything about my way of life."
Boone, who is entering his fourth season as the Yankees' manager, said he looks forward to "getting back to work in the next several days."
Yankees bench coach Carlos Mendoza served as interim manager for the team's exhibition game against the Toronto Blue Jays on Wednesday night in Tampa.
Boone played in MLB from 1997 to 2009 and was an All-Star selection with the Yankees in 2003. He took over as manager of the club in 2018.