An angry Milne hit out at Saints counterpart Stewart Gilmour after the Scottish Premier League failed to secure the 11-1 vote necessary to send the plan to the Scottish Football League.
The vote killed off a package that would have seen a merged 12-12-18 structure with extended play-offs, more equitable distribution of central income and a pyramid system allowing promotion from the non-league ranks.
Gilmour, who was on the SPL steering committee that came up with the plan, agreed in principle with the SFL in January, was first to leave Hampden after about four hours of talks.
St Mirren and County had both expressed concerns with the plan to split the top two leagues into three divisions of eight after 22 games - a scheme the SPL believed would generate extra income from television and sponsors but that the objectors feared could damage season ticket income.
Gilmour had also made it clear he was opposed to the retention of the 11-1 voting structure for protected issues, such as limits on the number of televised home games for each club.
However, Gilmour and County chairman Roy MacGregor rejected a compromise deal offering to change the democratic system for future league structure changes to 9-3 - a decision that left Milne fuming.
Milne said: "This is going to have major implications for Scottish football - it's going to potentially seriously damage the game in the long term.
"I'm very angry because I think today we have let down Scottish football.
"St Mirren Football Club have really got to pose themselves the question: why are they prepared to put the rest of Scottish football in jeopardy just because of their own selfish interests?
"This is a massive opportunity that has been blown, particularly on the whims of an individual.
"In that room, we've got to be in there with the interests of our club but we've got a wider responsibility for the SPL as an organisation and also wider Scottish football.
"None of that was displayed by Stewart Gilmour and St Mirren Football Club."
The Aberdeen chairman questioned what St Mirren's "agenda" was and claimed their decision to reject the reconstruction rules defied logic.
And that led Milne to believe that Gilmour's public concern about voting structures was disingenuous.
"It's just another red herring that Stewart continually threw on the table," he said.
"If it was so important, why was he not prepared to back the change that was offered on the table today, that future league reconstruction would be dealt with a normal 75 per cent vote the same as the rest of business?"
Milne claimed Gilmour had failed to properly explain his opposition and he added: "I'm disappointed in Ross County as well. It was stressed to (chairman) Roy MacGregor that he has a responsibility that goes beyond Ross County, he has a responsibility as part of the SPL set up to have wider interest in Scottish football."
MacGregor has not fully explained his opposition, although he argued at the weekend that ignoring the views of the club's fans and staff would be "suicide".
The problem is that SPL clubs do not want to give up money to First Division clubs without increasing the revenue, something most of them believed the middle-eight would achieve.
Clydesdale Bank's sponsorship deal expires this summer and it is thought that a replacement had been lined up on the basis of a new structure.
Milne said: "We are making life extremely difficult for ourselves. That is the reality of today's decision.
"It just simply increases the financial pressure on every single club.
"At the moment, insufficient money is coming into Scottish football.
"This provided us with an opportunity to start getting more money into the game.
"If we can't show faith in Scottish football, why would external sponsors show faith in Scottish football?
"This sends out an horrendous message to Scottish football and the wider community."