The 31-year-old Bulgarian looked set for a switch to Fiorentina earlier on Wednesday, 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 reportedly decide he wants to remain in England.
Marotta insisted Juve had "acted with the maximum fairness and transparency" towards Fiorentina, who earlier accused the Turin club of scuppering their deal for Berbatov with "reckless and arrogant actions".
"We have much to discuss with Fiorentina," Marotta said to Sky Sport Italia.
"We have acted with the maximum fairness and transparency with regard to the market dynamics.
"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."
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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.
"On Wednesday, 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 has scored 48 league goals at United, helping them to two Premier League titles, but his Old Trafford future has been in doubt since he was left out of the squad for the 2010-11 Champions League final against Barcelona at Wembley.
Despite slipping down the pecking order last year he reminded any potential suitors of his goalscoring class with a hat-trick against Wigan on Boxing Day, before adding two more in the unexpected home defeat to Blackburn five days later.
Last month he admitted he was resigned to leaving the club this summer, saying it would be "better for everyone" if he exited Old Trafford.