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.
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.
"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."