It is entitled Innocent Victims, a reference to Mr Al Fayed's belief - unsupported by any evidence, according to the inquest - that the couple were murdered on the orders of the Duke of Edinburgh.
The bronze figure shows the couple, who died in a vehicle crash in Paris in 1997, holding hands underneath a bird with its wings outstretched.
Harrods is now owned by the Qatari royal family.
The statue was designed by Harrods artistic design adviser Bill Mitchell, who had worked for the Fayed family for more than 40 years.
The iconic Knightsbridge department store, long a symbol of great opulence and extravagance, had enjoyed unrivalled financial success but since 2000 had lacked the one thing to which ambitious retailers aspire: a royal warrant.
Plane skids off runaway in northern Turkey, no injuries
The airport, situated in the Turkish province of the same name, was closed for several hours afterwards but has since reopened. The plane , belonging to private low-priced carrier Pegasus , had arrived from the capital Ankara.
The Queen had also dropped Harrods as her provider of Christmas puddings in favour of Tesco.
When the statue was unveiled, Fayed said it was a more "fitting tribute" to Diana than the official memorial fountain in Hyde Park that he described as a "sewer".
While the controversial statue remained in place, there had been little chance that Harrods would regain the favour of the British royals.
Mr Ward said "the time was right" to take down the shrine.
But the store's managing director, Michael Ward, said it was now time to return it, noting that Diana's sons Princes William and Harry were commissioning their own statue to their mother at Kensington Palace.