Lyon successfully appealed to Fifa to make Fulham pay the final instalment of a £11.5million fee for the French international after signing him in August 2001.
Fulham, who have appealed against this ruling, had baulked at paying the outstanding portion of the fee because they fear it will be pocketed by an agent.
Fifa have given Fulham until March 28 to pay the remainder of the fee or face a ban on future transfers.
The French club also sued Al Fayed because he had stood as personal guarantor in case the transfer fee was not paid.
Justice Stanley Burnton said he would stay the High Court proceedings, pending the resolution of Fifa's arbitration proceedings.
Burnton revealed that whatever the Fifa arbitration tribunal decided, it should put an end to the High Court action.
He has set a 14-day deadline for Al Fayed to pay the money into the court otherwise judgment will be entered against him.
"It seems to me that I am close to being willing to give judgement but that I should refrain from doing so to allow a shadowy defence to be argued," said Burnton.