The agreed sum of around £750,000 has still to be paid and the FA last night told the Barclays Premier League club that, for the time being, the only place they should send it is to the SFA.
The money will then be held by the Scottish ruling authority pending newco Rangers' application to join the SFA. Southampton announced 19 days ago they had signed the former Ibrox captain.
A fee was only agreed between the clubs last weekend, although no money has changed hands so far.
SportTimes under-stands that, instead of placing the money with the SFA, Southampton and Rangers have agreed to delay the financial transaction until membership is approved.
The FA intervened because of the uncertainty still hanging over Rangers.
Oldco Rangers were not entitled to the money because it sold the players' registrations to the newco, and the newco cannot take any money for Davis either because it is not a football club until it has SFA membership.
That impasse could be resolved as early as today after further talks between Rangers chief executive Charles Green, SFA chief executive Stewart Regan and SPL chief Neil Doncaster.
Once Rangers have SFA membership, the FA will be happy for Southampton to send the Davis money to Ibrox.
Green has tried to negotiate fees for most of the players who have left Ibrox this summer, but he was successful in doing so only with Davis and Saints.
Others – such as Everton with Steven Naismith and Norwich City with Steven Whittaker – opposed his view that players who refused to allow their contracts to be transferred from the oldco to the newco were in breach of contract.
And except for Southampton none agreed with him that Rangers were entitled to transfer fees for the departing players.
By agreeing a deal with Rangers, Southampton were able to process the deal without awaiting clearance from Fifa.