St Mirren and Ross County voted against the changes, which would have seen the league structure cut to three divisions of 12, 12 and 18 teams.
At Monday's meeting the clubs failed to secure the 11-1 majority needed to send the plans to the Scottish Football League.
Doncaster was disappointed that the proposals were snubbed by St Mirren and Ross County as he feels they were in the best interests of the game in Scotland.
"I think it was a real opportunity missed for the whole game," Doncaster told Sky Sports News. "So many of the things that supporters have said for so long now that they wanted to see a pyramid structure for the game in this country, more excitement, more meaningful games, play-offs, better distribution of revenues throughout a single league. All of those things which were part of the proposals they have now been lost."
Doncaster refused to divulge St Mirren's and Ross County's reasons for voting against the proposals, saying: "Well, you would have to ask them what their reasons were.
"There was a lot of speculation going into the meeting that it was all about voting change on league structure and of course one concession that was put forward within the meeting was that actually that should change and the hurdle league structure being changed in future should be lower from 11-1 to 9-3.
"But that wasn't enough and I think that surprised a number of people in the room even despite that concession there was still two against.
"It is not for me to talk about individual clubs. Ultimately I represent all 12 member clubs so you would have to ask each club the reasons they felt as they did.
"I am very disappointed on behalf of the whole game, but in particular the First Division clubs who stood to gain the most from these proposals.
"We all understand a strong second tier is important to any league and those clubs who are struggling to provide full-time professional football on very limited resources, those are the clubs who were relying on the SPL today to deliver a positive vote and they have been let down."