St Mirren and Ross County voted against the plan to restructure the current four-division set-up with three new divisions in a meeting at Hampden Park in Glasgow on Monday and it now seems likely the current structure will continue.
The new plan involved three leagues comprising two top divisions of 12 clubs and one lower division of 18 clubs with a complicated end of season playoff competition in which the top two divisions would split into three divisions of eight teams.
In a statement the Scottish Premier League expressed its unhappiness at the outcome of the vote.
Aberdeen chairman Stewart Milne said: "It's a no vote I am afraid and you need to ask one club in particular - St Mirren - exactly what their agenda is.
"Two clubs rejected the restructuring plans and no one else can see the logic behind that. This will have major implications for Scottish football and it is seriously going to damage the game in the long-term."
Ross County chairman Roy McGregor and his St Mirren counterpart Stewart Gilmour refused to answer reporters' questions.
Scottish football has suffered from falling crowd numbers and a drop in sponsorship and broadcasting revenue over recent years and the new restructuring plan was designed to bring some excitement and new corporate and revenue opportunities back to the game.
Premier League chairman Ralph Topping said: "An overwhelming majority of SPL clubs voted for these proposals to go through.
"The proposals foundered on the opposition of two clubs. The package involved concessions from all clubs and was for the betterment of Scottish football as a whole.
"Scottish football needs to change. I had previously announced my intention to step down once a successor had been identified. I have today advised the Board that I will not be seeking re-election at the SPL's AGM this July."