The 12 clubs had been meeting at Hampden today and had expected to defer any decision on a vote.
Rangers newco owner Charles Green and manager Ally McCoist arrived for the meeting together, although McCoist left shortly before noon as the talks continued.
The SPL announced news of the vote in a brief statement after more than five hours of talks at Hampden.
The 12 clubs had been meeting at Hampden today and had expected to defer any decision on a vote.
SPL chief executive Neil Doncaster earlier hinted the vote could be deferred amid fears over the financial consequences of the Ibrox club starting their new life in the Third Division, but clubs carried through their vow to deny Mr Green's bid.
An SPL statement read: "At today's General Meeting, SPL clubs today voted overwhelmingly to reject the application from Rangers newco to join the SPL."
SPL clubs will now hope their Scottish Football League counterparts accept the newco in the First Division amid warnings that £16million could be lost to the Scottish game if they go down to the Third.
Three-quarters of Rangers fans on the season-ticket database voted for the lower tier in a poll for their preferred option, but Green has previously declared his intention to play at the highest possible level.
Warnings have been made in the last few days that up to half the SPL clubs could go into administration if the Ibrox club are in the bottom tier.
It appears that most if not all of the SPL's commercial contracts include exit clauses for sponsors and partners allowing them to pull out or renegotiate if the Old Firm are not present.
The clauses were inserted amid speculation over the Glasgow pair moving to England or into a European league but they have proved costly after Rangers went into liquidation last month.
A package put to SFL clubs to accept the Ibrox side in the second tier includes moves to merge the leagues, promotion play-offs to the top flight and a £1million payment for television rights.
Before the meeting this morning, Doncaster said: "There are probably three options for dealing with Rangers. Rangers coming into the SPL with an appropriate range of sanctions is one option. Rangers going into the second tier is another option.
"The option that a lot of people have talked about, Rangers in the fourth tier, ultimately that would wreak huge financial damage on the whole game and it's difficult to see why 41 innocent clubs should pay the price for the misdeeds of one. So I think there are really two viable options that are in play at the moment."
It is as yet unclear whether relegated Dunfermline or Dundee, who finished second in the First Division, will replace Rangers in the SPL although the proposal put to SFL clubs states the Dens Park club would be promoted.
Green, whose Sevco firm bought the assets of Rangers for £5.5million, attended the meeting with chairman Malcolm Murray and McCoist. The verdict was announced by email about 2.20pm, with Green and Murray leaving shortly afterwards, while SPL clubs continued to talk.
Green claimed earlier this week he was confident chairmen would listen to his pleas after meeting several clubs to warn them of the financial implications.
Murray issued an "unreserved" apology yesterday in a move thought to be designed to pave the way for a U-turn. But St Johnstone, St Mirren, Aberdeen, Hearts, Hibernian, Dundee United and Inverness had already declared their opposition while Motherwell last night announced their fans had voted to reject the application. Green needed an 8-4 majority.
Meanwhile, Clyde have claimed that Scottish Football Association chief executive Stewart Regan effectively vowed to block a newco Rangers starting life in the SPL.
Regan denied the claims last night but Clyde say the Scottish Football League clubs were clearly left with just two options following a meeting yesterday - accept the Ibrox club in the Irn-Bru First Division or be subjected to an SPL2 breakaway to avoid the financial consequences of a Third Division entry.
Just before SPL clubs rejected the newco application, Clyde released a lengthy statement on their official website giving an eloquent account of the meeting and difficult situation placed on SFL clubs.
"There were a few new things learned in the meeting, not least that the rules of the SFL would allow any club accepted into the SFL, by a simple majority, to be placed in any division," the Third Division club said.
"The rules do not state, nor imply, that they must join at the bottom tier, only custom and practice around good governance and integrity has seen teams join in the bottom tier.
"In addition, the attendees at the meeting were left in absolutely no doubt whatsoever by Stewart Regan that if the SPL clubs voted to allow a newco into the SPL then it would be blocked by the SFA refusing to transfer the SFA membership.
"It was however caveated well enough to make it less than an absolute statement. The meeting was full of implied actions and outcomes, the use of clever language when delivering the speeches allows anyone to defend with 'that is not what I said'.
"However, nobody will have left the meeting with anything other than the very clear messages being put across. Denials of the substance of the message being delivered do not assist anyone in this absolutely dreadful situation."
Regan had said in a statement last night: "Unfortunately, a comment relating to one potential scenario Rangers FC's readmission to the SPL - was distorted, taken out of context and leaked to the media by a member.
"For the avoidance of doubt, any decision regarding the future status of Rangers FC requires not only the transfer of the SPL share but the transfer of the Scottish FA's membership.
"The Scottish FA board will approve this only when all relevant information has been provided and the directors are satisfied that the solution presented is in the best interests of Scottish football."
Clyde had previously stated their objection to voting Rangers into the First Division and they stuck to that stance today.
The Cumbernauld-based club said the consequences of refusing the plan would be a loss of the annual £2million settlement payment from the SPL.
They accused the SFA of "absent leadership" and added: "There will be no winners. Any level of integrity for the sport will be lost by one outcome and financial collapse, we are told, will fall upon the SPL with the other.
"The board of the SFL are being put under intolerable pressure by the other bodies looking to avoid the implications of properly applying their own governance procedures.
"In summary, the SFA implication is that there will be no entry to the SPL. The SPL implication is that it therefore has to be SFL1 with a bit of restructure, or an SPL2 with the rest of the SFL cut adrift. There were no other options.
"Whilst Stewart Regan said that the SFA did not favour an SPL2, there was no equivalent abhorrence of that proposal as was attached to the proposal for a newco in the SPL, leaving the implication that the door remains wide open for the SPL to secure their £16million with or without the SFL."
