Fayed's grandiose London department store refused to let the Ukrainian team in for a spot of souvenir shopping when they turned up in a large group wearing tracksuits.
Locked out: Shakhtar players were refused entry to Harrods
Fulham, also owned by the businessman, followed up the snub by beating Shakhtar 2-1 in the Europa League last 32 first leg.
But with the return match looming in Donetsk next Thursday, the UEFA Cup holders revealed Fayed had been building bridges.
The main man: Fulham chairman and Harrods owner Mohamed Al Fayed
'The store's owner has made apologies for that incident,' Shakhtar said on their website.
'Mohamed Al Fayed assured that there must have been some misunderstanding.
Fierce battle: Shakhtar Donetsk lost 2-1 at Craven Cottage in their first leg clash
'On the contrary, he would be happy to see Shakhtar players at his shops. The billionaire is very upset over this incident and made his apology.'
'Shakhtar's CEO Sergiy Palkin has let Rinat Akhmetov, the president of the club, know about such regrets. The apologies are accepted. The issue is settled.'
Fulham owner Al Fayed bans Shakhtar Donetsk players from his Harrods storeFulham 2 Shakhtar Donetsk 1: Bobby Zamora fires a dazzler to stun holders FULHAM FC