The tree, which suffered major damage from last week's ice storm, was removed over the weekend, the club confirmed Sunday.
The golf course is the site of the annual Masters Golf Tournament.
The loblolly pine, named after President Dwight Eisenhower, a club member, because of his propensity to hit into it when he played the course, was 65 feet tall and believed to be more than 100 years old.
"The loss of the Eisenhower Tree is difficult news to accept. We obtained opinions from the best arborists available, and, unfortunately, were advised that no recovery was possible," Augusta National and Masters chairman Billy Payne said in a statement.