The 31-year-old Bulgarian looked set for a switch to Fiorentina, having agreed terms with the Viola and been asked to head to Florence for a medical. However, Berbatov never arrived in Italy, prompting Fiorentina to accuse Serie A rivals Juve of hijacking the deal, only for the player to decide he wants to remain in England.
He has since arrived at Fulham for a medical, which was confirmed by the West London club.
Marotta insisted Juve had "acted with the maximum fairness and transparency" towards Fiorentina, and told Sky Sport Italia: "We have much to discuss with Fiorentina. We have acted with the maximum fairness and transparency with regard to the market dynamics."
He went on: "I reject the allegations from Fiorentina. We entered into the business over Berbatov when we heard that he had refused Fiorentina, and in the meantime there was a proposal by Fulham.
"We made our own, then the player said he preferred to stay in England for family reasons. It was not a rejection.
"We wanted to take advantage of an opportunity that had appeared to us in the market. Many teams were following the player."
A statement from Fiorentina earlier read: "ACF Fiorentina announces that the acquisition of Dimitar Berbatov finally fell through after an agreement had been reached with Manchester United [exchange of contract, the first instalment of the consideration paid and surety for the second instalment already signed] and after it had reached a verbal understanding with the player on his contract.
"During today, the English club granted its affiliated written permission for the player to travel to Florence for a medical and to sign the contract. [We thought] the player had embarked, accompanied by his attorney, on a flight - tickets paid for by Fiorentina - to Florence.
"But the player never arrived in Florence....because of reckless and arrogant actions of other companies, which have nothing to do with the values of honesty, fair play and ethics of sport and that lie beyond the boundaries of loyalty.
"As for the player, despite his characteristics and his technical merit, at this point we are happy that he did not come to Fiorentina. He did not deserve our city and our shirt and the values it represents."
Berbatov was reportedly swayed towards Fulham so he can work with Martin Jol, his former manager at Tottenham, and to stay in England with his young family.