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.
"It is not a feeling, it is a fact," he said. "It is a takeover. We are joining their company, their organisation.
"They have swallowed us up. 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."
SFL chief executive David Longmuir admitted there was some sadness behind the end of his organisation, saying ''yes and those feelings are heartfelt'' and also conceded that there were many misgivings among the clubs, even those who had voted yes.
"I feel there were some reluctant heroes today," he said. "We have always embraced the big principles but once you go behind the big principles like governance, distribution and one league body, there were areas of major concerns.
"But nevertheless a lot of them have seen it for the good of the game and we all accept that Scottish football is better governed under one roof.
"It is a means to an end. The only tangible benefit the fans are going to see are play-offs between the first (division) and the premier and the possible impact of a pyramid coming in at the end of 2014/15.
"It is not an end to itself. There is a lot more that needs to be done.
"On the 27th June there will be a formalised completion of the process and the first board meeting of the new organisation will take place that day and at that point a board will be appointed.
"I would imagine that other processes will take place to design the new organisation and resource it.''
Asked if he would have a role in the new organisation he replied: "That is something I am not considering at the moment until such times as the completion on June 27, and others will tell me if I have.''
Longmuir challenged the SPFL to carry on the good work of the SFL.
"Today's decision will lead to the winding up of the Scottish Football League as we currently know it, an organisation that has been the bedrock of our game for 123 years," he said.
"The legacy of the SFL will long be remembered and admired and we trust the custodians of the new body will continue to work in an open, trustworthy and professional manner at all times for the good of our national game."