St Mirren and Ross County vetoed proposals for a restructure of the Scottish game at an SPL meeting at Hampden, which required an 11-1 majority to send the plans to the Scottish Football League. Despite the outcome of the formal vote, Doncaster indicated he had no plans to step down from his own position.
He said: "I'm here for as long as the clubs want me to be here. I believe very much in the Scottish Premier League and I will do my utmost to continue to do the best by that league."
He added: "There is a lot of work to be done by the entire executive team over the summer. We've got sponsors to find. We need to bring as much money as we can in to benefit the SPL clubs and that work will continue."
The plans would have seen both league bodies merge in a 12-12-18 structure with a pyramid system below. The top two leagues would then split into three after 22 games in a bid to generate extra revenue, which would have been split more equitably with current First Division clubs.
Doncaster added: "I'm extremely disappointed for Scottish football as a whole.
"But I'm particularly disappointed for the First Division clubs, who were really relying on this vote today, relying on the SPL clubs allowing a redistribution of income that would have enabled clubs in the First Division to sustain full-time professional football in an environment where it's so difficult at the moment.
"That redistribution of money, the single league, the pyramid structure, play-offs - all of those benefits have now been denied us by this vote today."
All 12 clubs had previously reached unanimous agreement in principle on the proposals.
Asked why two clubs subsequently opted not to back the plans, Doncaster said: "That's a question you would need to ask individual clubs. What I can't do is talk about individual clubs and the way they voted or the reasons they voted that way. That's a conversation you will have to have with them."