The deadline north of the border is Saturday at 11pm, while clubs in England, for example, have until 11pm on Monday to negotiate deals on transfers.
An SFA spokesperson explained: "The window closes tomorrow because Saturday is a working day for our registration department.
"UEFA sent round a circular on June 21 saying that the deadline can be moved to the first working day after August 31.
"Saturday the 31st is a working day for us and there is something like 10 other associations who are all closing on the 31st as well."
Rangers are currently under a transfer embargo until August 31 after which date they can register the eight free agents who have commited to join the Light Blues.
Had the window been open until Monday, the Glasgow club would theoretically have been able to purchase new players in a 48-hour period instead of waiting until January.
Boss Ally McCoist said: "It's just something we have to accept. The SFA has made the decision and you would have to ask the SFA why they have made that decision.
"We just have to abide by the rules that the SFA put forward, which we will do.
"It probably stopped us by a couple of days possibly being able to purchase a player or two, I believe.
"But that's where we are. That's fine. I'm not totally shocked at the decision.
"You would have to ask the SFA why they made that decision but we are abiding by it, of course we will."
On Thursday, St Johnstone manager Tommy Wright claimed the "bizarre" decision to close the window on Saturday night could deny him his latest signing target as the player's English club want him to play an under-21 game on Monday before going on loan.
Hibernian manager Pat Fenlon also described the decision as "peculiar" given clubs are busy with games on Saturday.