All international transfers will have to got through FIFA's Transfer Matching System (TMS) from this Friday.
The world governing body believes the system will prevent money laundering, protect minors and make transfers more transparent.
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Clubs will have to declare whether there is any third party ownership of a player - the issue that caused the Carlos Tevez controversy at West Ham - or risk being sanctioned.
One aspect of the system is that as soon as the transfer deadline is passed, it shuts down and prevents any more transfer activity.
Mark Goddard, the general manager of TMS, told reporters: 'It's no longer a good idea to play a game of chicken in the negotiations for transfers.
'Over the last two and half years we have seen examples of big clubs like Real Madrid who last year came out very early in the transfer market and did their business in the first two weeks of the window.
Historic moment: Blatter believes the system will have a positive impact on the game
'They avoided leaving it until the last minute as they didn't want to risk playing a game of chicken with a computer system which would say time has run out.'
Goddard said there were no grey areas with the online system - for example when Tottenham signed Rafael van der Vaart from Real Madrid minutes before the transfer deadline, it was all done within the computer system's time limit.
On third-party ownership of players, Goddard said clubs risked sanctions ranging from fines to points deductions and transfer bans if they made false statements.
He added: 'For every single transfer it is mandatory for both clubs to declare that there are no third party influences on this transfer.
'That means we have an electronic record and if it appears that is not a truthful statement we can go back to the transfer in the system and remind the club or the association what they said on the record.'
More than 30 details on each transfer have to be entered, such as information on the player, club details, all payments including the amount, timing and bank details, as well as agents involved and the payments to them.
Documentary evidence backing up the details must also be uploaded onto the system.
The system will also keep track of individual players to ensure proper compensation payments for clubs that have trained young players but have then seen them transferred.
FIFA president Sepp Blatter said: 'This is a historic moment for football. TMS is a relatively simple online system but it will have a tremendous impact on the international transfer of players.
'Thanks to TMS, football's authorities have more details available on each and every transfer. The most important thing is that it increases the transparency of individual transactions and helps us to tackle issues such as the fight against money laundering and the protection of minors in transfers.'
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