At a special general meeting at Hampden Park, 23 out of 29 SFL clubs - one more than required - voted for reconstruction plans which included one governing body. Rangers did not get a vote as they are associate members having joined last summer.
It was widely perceived that the new governing body - to be called the Scottish Professional Football League - would be the result of a merger but Ballantyne was strident when asked if he felt it was more of a takeover. He said: "It is not a feeling, it is a fact. It is a takeover. We are joining their company, their organisation. They have swallowed us up."
He added: "We could use nice words about it, but it is a takeover.
"The original plan and discussion going back many months was for a new merged body but as things went on it became clear that that wasn't going to happen. There was a positive vote today regarding yes and no but a lot of people left the room with a heavy heart.
"It is very sad that the Scottish Football League has had to be a casualty but unfortunately we were left with one option.
"Did I want to see the end of the Scottish Football League? Absolutely not. Did I want to see football strive forward? Then yes. It will be for others to decide if this step takes us to where we want to go.''
The proposals also include a 12-10-10-10 structure, with the 11th-placed team in the top-flight taking part in four-team play-offs at the end of the campaign and a new financial redistribution model.
The vote, though, took place amid a background of acrimony due, in part, to the ever-present threat of a breakaway by the first division clubs. Ballantyne revealed that clubs were only sent due diligence reports at 5pm on Monday night.
He said: "That is not a criticism, that is a fact and the clubs had to take that into account and they did that. We have been looking for due diligence for a long, long time but for whatever reason it wasn't available to us. Whether it was long enough or not is irrelevant, that's what we had and that's what the clubs used in their decision-making process."